Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Complexes of RNA-binding proteins with ribonucleic acids (RNA).
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
A family of ribonucleoproteins that were originally found as proteins bound to nascent RNA transcripts in the form of ribonucleoprotein particles. Although considered ribonucleoproteins they are primarily classified by their protein component. They are involved in a variety of processes such as packaging of RNA and RNA TRANSPORT within the nucleus. A subset of heterogeneous-nuclear ribonucleoproteins are involved in additional functions such as nucleocytoplasmic transport (ACTIVE TRANSPORT, CELL NUCLEUS) of RNA and mRNA stability in the CYTOPLASM.
Proteins that bind to the 3' polyadenylated region of MRNA. When complexed with RNA the proteins serve an array of functions such as stabilizing the 3' end of RNA, promoting poly(A) synthesis and stimulating mRNA translation.
Ribonucleic acid that makes up the genetic material of viruses.
A family of RNA-binding proteins that are homologues of ELAV protein, Drosophila. They were initially identified in humans as the targets of autoantibodies in patients with PARANEOPLASTIC ENCEPHALOMYELITIS. They are thought to regulate GENE EXPRESSION at the post-transcriptional level.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.
A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).
The parts of a macromolecule that directly participate in its specific combination with another molecule.
A family of double-stranded RNA-binding proteins that are related to NFATC TRANSCRIPTION FACTORS. In addition to binding to RNA, nuclear factor 90 proteins form heterodimeric complexes that regulate GENETIC TRANSCRIPTION and may play a role in T-CELL activation.
Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
A class of closely related heterogeneous-nuclear ribonucleoproteins of approximately 34-40 kDa in size. Although they are generally found in the nucleoplasm, they also shuttle between the nucleus and the cytoplasm. Members of this class have been found to have a role in mRNA transport, telomere biogenesis and RNA SPLICING.
A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.
RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Transport proteins that carry specific substances in the blood or across cell membranes.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
A protein subunit that takes part in forming nuclear factor 90 protein complexes.
A family of proteins that promote unwinding of RNA during splicing and translation.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
A heterogeneous-nuclear ribonucleoprotein that has specificity for AU-rich elements found in the 3'-region of mRNA and may play a role in RNA stability. Several isoforms of hnRNP D protein have been found to occur due to alternative mRNA splicing (RNA SPLICING).
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
A multifunctional heterogeneous-nuclear ribonucleoprotein that may play a role in homologous DNA pairing and recombination. The N-terminal portion of protein is a potent transcriptional activator, while the C terminus is required for RNA binding. The name FUS refers to the fact that genetic recombination events result in fusion oncogene proteins (ONCOGENE PROTEINS, FUSION) that contain the N-terminal region of this protein. These fusion proteins have been found in myxoid liposarcoma (LIPOSARCOMA, MYXOID) and acute myeloid leukemia.
A RNA-binding protein that binds to polypyriminidine rich regions in the INTRONS of messenger RNAs. Polypyrimidine tract-binding protein may be involved in regulating the ALTERNATIVE SPLICING of mRNAs since its presence on an intronic RNA region that is upstream of an EXON inhibits the splicing of the exon into the final mRNA product.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.
Ribonucleic acid in chloroplasts having regulatory and catalytic roles as well as involvement in protein synthesis.
Established cell cultures that have the potential to propagate indefinitely.
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
Factors that are involved in directing the cleavage and POLYADENYLATION of the of MESSENGER RNA near the site of the RNA 3' POLYADENYLATION SIGNALS.
The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) adds 60-200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here.
Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).
Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)
An integration host factor that was originally identified as a bacterial protein required for the integration of bacteriophage Q beta (ALLOLEVIVIRUS). Its cellular function may be to regulate mRNA stability and processing in that it binds tightly to poly(A) RNA and interferes with ribosome binding.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
A large family of RNA helicases that share a common protein motif with the single letter amino acid sequence D-E-A-D (Asp-Glu-Ala-Asp). In addition to RNA helicase activity, members of the DEAD-box family participate in other aspects of RNA metabolism and regulation of RNA function.
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
Viruses whose genetic material is RNA.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
A group of closely related heterogeneous-nuclear ribonucleoproteins of approximately 41-43 kDa in size found in the cell nucleus. Members of this class have been implicated in a variety of processes including splicing, polyadenylation, and nuclear retention of RNA.
RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.
The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.
RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.
Proteins prepared by recombinant DNA technology.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
A poly(A) binding protein that has a variety of functions such as mRNA stabilization and protection of RNA from nuclease activity. Although poly(A) binding protein I is considered a major cytoplasmic RNA-binding protein it is also found in the CELL NUCLEUS and may be involved in transport of mRNP particles.
A family of immunophilin proteins that bind to the immunosuppressive drugs TACROLIMUS (also known as FK506) and SIROLIMUS. EC 5.2.1.-
Small kinetoplastid mitochondrial RNA that plays a major role in RNA EDITING. These molecules form perfect hybrids with edited mRNA sequences and possess nucleotide sequences at their 5'-ends that are complementary to the sequences of the mRNA's immediately downstream of the pre-edited regions.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
An endoribonuclease that is specific for double-stranded RNA. It plays a role in POST-TRANSCRIPTIONAL RNA PROCESSING of pre-RIBOSOMAL RNA and a variety of other RNA structures that contain double-stranded regions.
Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC
Proteins involved in the process of transporting molecules in and out the cell nucleus. Included here are: NUCLEOPORINS, which are membrane proteins that form the NUCLEAR PORE COMPLEX; KARYOPHERINS, which carry molecules through the nuclear pore complex; and proteins that play a direct role in the transport of karyopherin complexes through the nuclear pore complex.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.
Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.
A ZINC FINGER MOTIF containing transcription factor that was originally identified as one of the IMMEDIATE-EARLY PROTEINS. It shuttles between the CYTOPLASM and the CELL NUCLEUS and is involved in destabilization of mRNAs for TUMOR NECROSIS FACTOR-ALPHA.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Proteins that regulate cellular and organismal iron homeostasis. They play an important biological role by maintaining iron levels that are adequate for metabolic need, but below the toxicity threshold.
Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.
A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.
Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.
Nucleic acid structures found on the 5' end of eukaryotic cellular and viral messenger RNA and some heterogeneous nuclear RNAs. These structures, which are positively charged, protect the above specified RNAs at their termini against attack by phosphatases and other nucleases and promote mRNA function at the level of initiation of translation. Analogs of the RNA caps (RNA CAP ANALOGS), which lack the positive charge, inhibit the initiation of protein synthesis.
Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.
The processes of RNA tertiary structure formation.
RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.
A family of soluble proteins that bind insulin-like growth factors and modulate their biological actions at the cellular level. (Int J Gynaecol Obstet 1992;39(1):3-9)
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
The aggregation of soluble ANTIGENS with ANTIBODIES, alone or with antibody binding factors such as ANTI-ANTIBODIES or STAPHYLOCOCCAL PROTEIN A, into complexes large enough to fall out of solution.
A RNA-binding protein that is found predominately in the CYTOPLASM. It helps regulate GENETIC TRANSLATION in NEURONS and is absent or under-expressed in FRAGILE X SYNDROME.
Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
Deletion of sequences of nucleic acids from the genetic material of an individual.
Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.
Proteins found in any species of bacterium.
Proteins obtained from various species of Xenopus. Included here are proteins from the African clawed frog (XENOPUS LAEVIS). Many of these proteins have been the subject of scientific investigations in the area of MORPHOGENESIS and development.
Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
Highly conserved nuclear RNA-protein complexes that function in RNA processing in the nucleus, including pre-mRNA splicing and pre-mRNA 3'-end processing in the nucleoplasm, and pre-rRNA processing in the nucleolus (see RIBONUCLEOPROTEINS, SMALL NUCLEOLAR).
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.
The sum of the weight of all the atoms in a molecule.
A multiribosomal structure representing a linear array of RIBOSOMES held together by messenger RNA; (RNA, MESSENGER); They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
A species of fruit fly much used in genetics because of the large size of its chromosomes.
The rate dynamics in chemical or physical systems.
A hemoflagellate subspecies of parasitic protozoa that causes nagana in domestic and game animals in Africa. It apparently does not infect humans. It is transmitted by bites of tsetse flies (Glossina).
Organelles in which the splicing and excision reactions that remove introns from precursor messenger RNA molecules occur. One component of a spliceosome is five small nuclear RNA molecules (U1, U2, U4, U5, U6) that, working in conjunction with proteins, help to fold pieces of RNA into the right shapes and later splice them into the message.
An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.
Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.
Intracellular proteins that reversibly bind hydrophobic ligands including: saturated and unsaturated FATTY ACIDS; EICOSANOIDS; and RETINOIDS. They are considered a highly conserved and ubiquitously expressed family of proteins that may play a role in the metabolism of LIPIDS.
Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.
Proteins found in any species of virus.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
Proteins obtained from ESCHERICHIA COLI.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
Proteins found in any species of protozoan.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.
Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.
The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport.
Gated transport mechanisms by which proteins or RNA are moved across the NUCLEAR MEMBRANE.
Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.
A cell line generated from human embryonic kidney cells that were transformed with human adenovirus type 5.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.
A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.
Proteins from the nematode species CAENORHABDITIS ELEGANS. The proteins from this species are the subject of scientific interest in the area of multicellular organism MORPHOGENESIS.
A poly(A) binding protein that is involved in promoting the extension of the poly A tails of MRNA. The protein requires a minimum of ten ADENOSINE nucleotides in order for binding to mRNA. Once bound it works in conjunction with CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR to stimulate the rate of poly A synthesis by POLY A POLYMERASE. Once poly-A tails reach around 250 nucleotides in length poly(A) binding protein II no longer stimulates POLYADENYLATION. Mutations within a GCG repeat region in the gene for poly(A) binding protein II have been shown to cause the disease MUSCULAR DYSTROPHY, OCULOPHARYNGEAL.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Antigens on surfaces of cells, including infectious or foreign cells or viruses. They are usually protein-containing groups on cell membranes or walls and may be isolated.
Protein analogs and derivatives of the Aequorea victoria green fluorescent protein that emit light (FLUORESCENCE) when excited with ULTRAVIOLET RAYS. They are used in REPORTER GENES in doing GENETIC TECHNIQUES. Numerous mutants have been made to emit other colors or be sensitive to pH.
A species of nematode that is widely used in biological, biochemical, and genetic studies.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
A dsRNA-activated cAMP-independent protein serine/threonine kinase that is induced by interferon. In the presence of dsRNA and ATP, the kinase autophosphorylates on several serine and threonine residues. The phosphorylated enzyme catalyzes the phosphorylation of the alpha subunit of EUKARYOTIC INITIATION FACTOR-2, leading to the inhibition of protein synthesis.
That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.
A cell line derived from cultured tumor cells.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
A family of RNA-binding proteins that has specificity for MICRORNAS and SMALL INTERFERING RNA molecules. The proteins take part in RNA processing events as core components of RNA-induced silencing complex.
A family of proteins involved in NUCLEOCYTOPLASMIC TRANSPORT. Karyopherins are heteromeric molecules composed two major types of components, ALPHA KARYOPHERINS and BETA KARYOPHERINS, that function together to transport molecules through the NUCLEAR PORE COMPLEX. Several other proteins such as RAN GTP BINDING PROTEIN and CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN bind to karyopherins and participate in the transport process.
One of the six homologous soluble proteins that bind insulin-like growth factors (SOMATOMEDINS) and modulate their mitogenic and metabolic actions at the cellular level.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
Proteins found in any species of fungus.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.
Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
Periplasmic proteins that scavenge or sense diverse nutrients. In the bacterial environment they usually couple to transporters or chemotaxis receptors on the inner bacterial membrane.
Proteins to which calcium ions are bound. They can act as transport proteins, regulator proteins, or activator proteins. They typically contain EF HAND MOTIFS.
The process of germ cell development in the female from the primordial germ cells through OOGONIA to the mature haploid ova (OVUM).
Nuclear nonribosomal RNA larger than about 1000 nucleotides, the mass of which is rapidly synthesized and degraded within the cell nucleus. Some heterogeneous nuclear RNA may be a precursor to mRNA. However, the great bulk of total hnRNA hybridizes with nuclear DNA rather than with mRNA.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
RNA present in neoplastic tissue.
A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.
Condensed areas of cellular material that may be bounded by a membrane.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
An aquatic genus of the family, Pipidae, occurring in Africa and distinguished by having black horny claws on three inner hind toes.
The artificial induction of GENE SILENCING by the use of RNA INTERFERENCE to reduce the expression of a specific gene. It includes the use of DOUBLE-STRANDED RNA, such as SMALL INTERFERING RNA and RNA containing HAIRPIN LOOP SEQUENCE, and ANTI-SENSE OLIGONUCLEOTIDES.
A nuclear RNA-protein complex that plays a role in RNA processing. In the nucleoplasm, the U1 snRNP along with other small nuclear ribonucleoproteins (U2, U4-U6, and U5) assemble into SPLICEOSOMES that remove introns from pre-mRNA by splicing. The U1 snRNA forms base pairs with conserved sequence motifs at the 5'-splice site and recognizes both the 5'- and 3'-splice sites and may have a fundamental role in aligning the two sites for the splicing reaction.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
A broad category of carrier proteins that play a role in SIGNAL TRANSDUCTION. They generally contain several modular domains, each of which having its own binding activity, and act by forming complexes with other intracellular-signaling molecules. Signal-transducing adaptor proteins lack enzyme activity, however their activity can be modulated by other signal-transducing enzymes
Female germ cells derived from OOGONIA and termed OOCYTES when they enter MEIOSIS. The primary oocytes begin meiosis but are arrested at the diplotene state until OVULATION at PUBERTY to give rise to haploid secondary oocytes or ova (OVUM).
A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.
A general transcription factor that plays a major role in the activation of eukaryotic genes transcribed by RNA POLYMERASES. It binds specifically to the TATA BOX promoter element, which lies close to the position of transcription initiation in RNA transcribed by RNA POLYMERASE II. Although considered a principal component of TRANSCRIPTION FACTOR TFIID it also takes part in general transcription factor complexes involved in RNA POLYMERASE I and RNA POLYMERASE III transcription.
A 12-KDa tacrolimus binding protein that is found associated with and may modulate the function of calcium release channels. It is a peptidyl-prolyl cis/trans isomerase which is inhibited by both tacrolimus (commonly called FK506) and SIROLIMUS.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
A family of secreted multidomain proteins that were originally identified by their association with the latent form of TRANSFORMING GROWTH FACTORS. They interact with a variety of EXTRACELLULAR MATRIX PROTEINS and may play a role in the regulation of TGB-beta bioavailability.
A species of GREEN ALGAE. Delicate, hairlike appendages arise from the flagellar surface in these organisms.
Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
Methods for determining interaction between PROTEINS.
The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.
Interruption or suppression of the expression of a gene at transcriptional or translational levels.
The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.

Apontic binds the translational repressor Bruno and is implicated in regulation of oskar mRNA translation. (1/12081)

The product of the oskar gene directs posterior patterning in the Drosophila oocyte, where it must be deployed specifically at the posterior pole. Proper expression relies on the coordinated localization and translational control of the oskar mRNA. Translational repression prior to localization of the transcript is mediated, in part, by the Bruno protein, which binds to discrete sites in the 3' untranslated region of the oskar mRNA. To begin to understand how Bruno acts in translational repression, we performed a yeast two-hybrid screen to identify Bruno-interacting proteins. One interactor, described here, is the product of the apontic gene. Coimmunoprecipitation experiments lend biochemical support to the idea that Bruno and Apontic proteins physically interact in Drosophila. Genetic experiments using mutants defective in apontic and bruno reveal a functional interaction between these genes. Given this interaction, Apontic is likely to act together with Bruno in translational repression of oskar mRNA. Interestingly, Apontic, like Bruno, is an RNA-binding protein and specifically binds certain regions of the oskar mRNA 3' untranslated region.  (+info)

Meiosis: MeiRNA hits the spot. (2/12081)

The protein Mei2 performs at least two functions required in fission yeast for the switch from mitotic to meiotic cell cycles. One of these functions also requires meiRNA. It appears that meiRNA targets Mei2 to the nucleus, where it can promote the first meiotic division.  (+info)

The splicing factor-associated protein, p32, regulates RNA splicing by inhibiting ASF/SF2 RNA binding and phosphorylation. (3/12081)

The cellular protein p32 was isolated originally as a protein tightly associated with the essential splicing factor ASF/SF2 during its purification from HeLa cells. ASF/SF2 is a member of the SR family of splicing factors, which stimulate constitutive splicing and regulate alternative RNA splicing in a positive or negative fashion, depending on where on the pre-mRNA they bind. Here we present evidence that p32 interacts with ASF/SF2 and SRp30c, another member of the SR protein family. We further show that p32 inhibits ASF/SF2 function as both a splicing enhancer and splicing repressor protein by preventing stable ASF/SF2 interaction with RNA, but p32 does not block SRp30c function. ASF/SF2 is highly phosphorylated in vivo, a modification required for stable RNA binding and protein-protein interaction during spliceosome formation, and this phosphorylation, either through HeLa nuclear extracts or through specific SR protein kinases, is inhibited by p32. Our results suggest that p32 functions as an ASF/SF2 inhibitory factor, regulating ASF/SF2 RNA binding and phosphorylation. These findings place p32 into a new group of proteins that control RNA splicing by sequestering an essential RNA splicing factor into an inhibitory complex.  (+info)

Selection and characterization of pre-mRNA splicing enhancers: identification of novel SR protein-specific enhancer sequences. (4/12081)

Splicing enhancers are RNA sequences required for accurate splice site recognition and the control of alternative splicing. In this study, we used an in vitro selection procedure to identify and characterize novel RNA sequences capable of functioning as pre-mRNA splicing enhancers. Randomized 18-nucleotide RNA sequences were inserted downstream from a Drosophila doublesex pre-mRNA enhancer-dependent splicing substrate. Functional splicing enhancers were then selected by multiple rounds of in vitro splicing in nuclear extracts, reverse transcription, and selective PCR amplification of the spliced products. Characterization of the selected splicing enhancers revealed a highly heterogeneous population of sequences, but we identified six classes of recurring degenerate sequence motifs five to seven nucleotides in length including novel splicing enhancer sequence motifs. Analysis of selected splicing enhancer elements and other enhancers in S100 complementation assays led to the identification of individual enhancers capable of being activated by specific serine/arginine (SR)-rich splicing factors (SC35, 9G8, and SF2/ASF). In addition, a potent splicing enhancer sequence isolated in the selection specifically binds a 20-kDa SR protein. This enhancer sequence has a high level of sequence homology with a recently identified RNA-protein adduct that can be immunoprecipitated with an SRp20-specific antibody. We conclude that distinct classes of selected enhancers are activated by specific SR proteins, but there is considerable sequence degeneracy within each class. The results presented here, in conjunction with previous studies, reveal a remarkably broad spectrum of RNA sequences capable of binding specific SR proteins and/or functioning as SR-specific splicing enhancers.  (+info)

Substrate specificities of SR proteins in constitutive splicing are determined by their RNA recognition motifs and composite pre-mRNA exonic elements. (5/12081)

We report striking differences in the substrate specificities of two human SR proteins, SF2/ASF and SC35, in constitutive splicing. beta-Globin pre-mRNA (exons 1 and 2) is spliced indiscriminately with either SR protein. Human immunodeficiency virus tat pre-mRNA (exons 2 and 3) and immunoglobulin mu-chain (IgM) pre-mRNA (exons C3 and C4) are preferentially spliced with SF2/ASF and SC35, respectively. Using in vitro splicing with mutated or chimeric derivatives of the tat and IgM pre-mRNAs, we defined specific combinations of segments in the downstream exons, which mediate either positive or negative effects to confer SR protein specificity. A series of recombinant chimeric proteins consisting of domains of SF2/ASF and SC35 in various combinations was used to localize trans-acting domains responsible for substrate specificity. The RS domains of SF2/ASF and SC35 can be exchanged without effect on substrate specificity. The RNA recognition motifs (RRMs) of SF2/ASF are active only in the context of a two-RRM structure, and RRM2 has a dominant role in substrate specificity. In contrast, the single RRM of SC35 can function alone, but its substrate specificity can be influenced by the presence of an additional RRM. The RRMs behave as modules that, when present in different combinations, can have positive, neutral, or negative effects on splicing, depending upon the specific substrate. We conclude that SR protein-specific recognition of specific positive and negative pre-mRNA exonic elements via one or more RRMs is a crucial determinant of the substrate specificity of SR proteins in constitutive splicing.  (+info)

A human sequence homologue of Staufen is an RNA-binding protein that is associated with polysomes and localizes to the rough endoplasmic reticulum. (6/12081)

In the course of a two-hybrid screen with the NS1 protein of influenza virus, a human clone capable of coding for a protein with high homology to the Staufen protein from Drosophila melanogaster (dmStaufen) was identified. With these sequences used as a probe, cDNAs were isolated from a lambda cDNA library. The encoded protein (hStaufen-like) contained four double-stranded RNA (dsRNA)-binding domains with 55% similarity and 38% identity to those of dmStaufen, including identity at all residues involved in RNA binding. A recombinant protein containing all dsRNA-binding domains was expressed in Escherichia coli as a His-tagged polypeptide. It showed dsRNA binding activity in vitro, with an apparent Kd of 10(-9) M. Using a specific antibody, we detected in human cells a major form of the hStaufen-like protein with an apparent molecular mass of 60 to 65 kDa. The intracellular localization of hStaufen-like protein was investigated by immunofluorescence using a series of markers for the cell compartments. Colocalization was observed with the rough endoplasmic reticulum but not with endosomes, cytoskeleton, or Golgi apparatus. Furthermore, sedimentation analyses indicated that hStaufen-like protein associates with polysomes. These results are discussed in relation to the possible functions of the protein.  (+info)

Mammalian staufen is a double-stranded-RNA- and tubulin-binding protein which localizes to the rough endoplasmic reticulum. (7/12081)

Staufen (Stau) is a double-stranded RNA (dsRNA)-binding protein involved in mRNA transport and localization in Drosophila. To understand the molecular mechanisms of mRNA transport in mammals, we cloned human (hStau) and mouse (mStau) staufen cDNAs. In humans, four transcripts arise by differential splicing of the Stau gene and code for two proteins with different N-terminal extremities. In vitro, hStau and mStau bind dsRNA via each of two full-length dsRNA-binding domains and tubulin via a region similar to the microtubule-binding domain of MAP-1B, suggesting that Stau cross-links cytoskeletal and RNA components. Immunofluorescent double labeling of transfected mammalian cells revealed that Stau is localized to the rough endoplasmic reticulum (RER), implicating this RNA-binding protein in mRNA targeting to the RER, perhaps via a multistep process involving microtubules. These results are the first demonstration of the association of an RNA-binding protein in addition to ribosomal proteins, with the RER, implicating this class of proteins in the transport of RNA to its site of translation.  (+info)

NMD3 encodes an essential cytoplasmic protein required for stable 60S ribosomal subunits in Saccharomyces cerevisiae. (8/12081)

A mutation in NMD3 was found to be lethal in the absence of XRN1, which encodes the major cytoplasmic exoribonuclease responsible for mRNA turnover. Molecular genetic analysis of NMD3 revealed that it is an essential gene required for stable 60S ribosomal subunits. Cells bearing a temperature-sensitive allele of NMD3 had decreased levels of 60S subunits at the nonpermissive temperature which resulted in the formation of half-mer polysomes. Pulse-chase analysis of rRNA biogenesis indicated that 25S rRNA was made and processed with kinetics similar to wild-type kinetics. However, the mature RNA was rapidly degraded, with a half-life of 4 min. Nmd3p fractionated as a cytoplasmic protein and sedimented in the position of free 60S subunits in sucrose gradients. These results suggest that Nmd3p is a cytoplasmic factor required for a late cytoplasmic assembly step of the 60S subunit but is not a ribosomal protein. Putative orthologs of Nmd3p exist in Drosophila, in nematodes, and in archaebacteria but not in eubacteria. The Nmd3 protein sequence does not contain readily recognizable motifs of known function. However, these proteins all have an amino-terminal domain containing four repeats of Cx2C, reminiscent of zinc-binding proteins, implicated in nucleic acid binding or protein oligomerization.  (+info)

There are a growing number of reports on the sub-physiological temperature culturing of mammalian cells for increased recombinant protein yields. However, the effect varies and the reasons for the enhancement are not fully elucidated. Expression of cold-inducible RNA-binding protein (cirp, also called cirbp or hnRNP A18) is known to be induced in response to mild, but not severe, hypothermia in mammalian cells. To clarify the molecular mechanism underlying the induction and to exploit this to improve the productivity of recombinant proteins, we tried to identify the regulatory sequence(s) in the 5′ flanking region of the mouse cirp gene. By transiently transfecting HEK293 cells with plasmids expressing chloramphenicol acetyltransferase as a reporter, we found that the cirp 5′ flanking region octanucleotide 5′-TCCCCGCC-3′ is a mild-cold responsive element (MCRE). When 3 copies of MCRE were placed upstream of the CMV promoter and used in transient transfection, reporter gene expression was
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TY - JOUR. T1 - Serine 195 phosphorylation in the RNA-binding protein Rbm38 increases p63 expression by modulating Rbm38s interaction with the Ago2-miR203 complex. AU - Zhang, Yanhong. AU - Feng, Xiuli. AU - Sun, Wenqiang. AU - Zhang, Jin. AU - Chen, Xinbin. PY - 2019/1/1. Y1 - 2019/1/1. N2 - The p63 transcription factor, a p53 family protein, regulates genes involved in various cellular processes, including cell growth and differentiation. We previously showed that RNA-binding motif protein (Rbm38) is a p63 target and, in turn, regulates p63 mRNA stability by binding to the AU/U-rich element in its 3UTR. Interestingly, Rbm38 can be phosphorylated at serine 195, altering its ability to regulate mRNA translation. However, whether the Ser-195 phosphorylation affects Rbm38s ability to destabilize p63 mRNA remains unclear. Here, using MCF7 and HaCaT cells, we showed that ectopic expression of phosphomimetic Rbm38-S195D increases, whereas WT Rbm38 and nonphosphorylatable Rbm38-S195A decrease p63 ...
RNA-binding proteins have diverse functions in the regulation of gene expression. This is the first report, to our knowledge, that a KH motif RNA-binding protein is regulated by p53 and that it serves as a mediator in inducing apoptosis and cell cycle arrest in G2-M. We have demonstrated that deletion of either of the KH domains or a point mutation in the C-terminal KH domain of MCG10as abrogates or severely diminishes the activity of MCG10 and MCG10as in binding RNA. As a result, the MCG10 and MCG10as mutants defective in RNA binding are also defective in inducing apoptosis and cell cycle arrest. These results indicate that, like other RNA-binding proteins, the RNA-binding activity is critical for the function of MCG10 and MCG10as. Interestingly, a 55-amino-acid insertion in the N-terminal KH domain does not interfere with the RNA-binding activity of MCG10.. Previously, we and others have shown that p53 cellular target genes are differentially regulated by p73 (21, 50, 107). We found that the ...
RNA-binding proteins are a critical component of the cellular machinery that dictate the fate of RNA molecules. As RNA virus genomes are small, they rely on host RNA-binding proteins to control the life of the viral RNA. However, which of these host proteins are required for virus infection remains largely unknown. Alfredos group developed a novel technique called comparative RNA interactome capture to interrogate which RNA-binding proteins are involved in the infection of a model virus called Sindbis (SINV). This work uncovered that SINV infection alters the activity of more than 200 cellular RNA-binding proteins, thus rewiring cellular RNA metabolism (Figure 1). ...
BACKGROUND: Low nuclear expression of the RNA-binding motif protein 3 (RBM3) has previously been found to be associated with poor prognosis in several cancer forms e.g. breast, ovarian, colorectal, prostate cancer and malignant melanoma. The aim of this study was to examine the prognostic impact of RBM3 expression in urinary bladder cancer.. METHODS: Immunohistochemical RBM3 expression was examined in tumours from 343 patients with urothelial bladder cancer. Chi-square and Spearmans correlation tests were applied to explore associations between RBM3 expression and clinicopathological characteristics. The impact of RBM3 expression on disease-specific survival (DSS), 5-year overall survival (OS) and progression-free survival (PFS) was assessed by Kaplan-Meier analysis and Cox proportional hazards modelling.. RESULTS: Reduced nuclear RBM3 expression was significantly associated with more advanced tumour (T) stage (p ,0.001) and high grade tumours (p=0.004). Negative RBM3 expression was associated ...
p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.,/p> ,p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.,/p> ,p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).,/p> ,p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x,sup>64,/sup> + x,sup>4,/sup> + x,sup>3,/sup> + x + 1. The algorithm is described in the ISO 3309 standard. ,/p> ,p class=publication>Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.,br /> ,strong>Cyclic redundancy and other checksums,/strong>,br /> ,a href=>Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993),/a>),/p> Checksum:i ...
In eukaryotic cells, a multitude of RNA-binding proteins play key roles in the posttranscriptional regulation of gene expression. Characterization of these proteins has led to the identification of several RNA-binding motifs, and recent experiments have begun to illustrate how several of them bind RNA. The significance of these interactions is reflected in the recent discoveries that several human and other vertebrate genetic disorders are caused by aberrant expression of RNA-binding proteins. The major RNA-binding motifs are described and examples of how they may function are given. ...
TY - JOUR. T1 - She2p is a novel RNA binding protein with a basic helical hairpin motif. AU - Niessing, Dierk. AU - Hüttelmaier, Stefan. AU - Zenklusen, Daniel. AU - Singer, Robert H.. AU - Burley, Stephen K.. PY - 2004/11/12. Y1 - 2004/11/12. N2 - Selective transport of mRNAs in ribonucleoprotein particles (mRNP) ensures asymmetric distribution of information within and among eukaryotic cells. Actin-dependent transport of ASH1 mRNA in yeast represents one of the best-characterized examples of mRNP translocation. Formation of the ASH1 mRNP requires recognition of zip code elements by the RNA binding protein She2p. We determined the X-ray structure of She2p at 1.95 Å resolution. She2p is a member of a previously unknown class of nucleic acid binding proteins, composed of a single globular domain with a five α helix bundle that forms a symmetric homodimer. After demonstrating potent, dimer-dependent RNA binding in vitro, we mapped the RNA binding surface of She2p to a basic helical hairpin in ...
Expression of the RNA-binding protein RBM3 is associated with a favourable prognosis and cisplatin sensitivity in epithelial ovarian cancer. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Author: Maatz, H. et al.; Genre: Journal Article; Published in Print: 2014-08; Open Access; Title: RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing
The protamine mRNAs are stored for up to 8 days as translationally repressed ribonucleoprotein particles during murine spermatogenesis. Translational repression of the protamine 1, Prm1, mRNA is controlled by sequences in its 3-untranslated region (UTR). In this study we used the yeast three-hybrid system to clone Msy4, which encodes a novel member of the Y box family of nucleic acid binding proteins. MSY4 specifically binds to a site within the 5 most 37 nucleotides in the Prm1 3 UTR. Msy4 is highly expressed in the testis, and the protein is detected in the cytoplasm of germ cells in both the testis and the ovary, where repressed messages are stored. Analysis of a previously described 48/50-kDa binding activity in testis extracts by electrophoretic mobility shift assays and immunoprecipitation indicates the activity is composed of MSY4 and MSY2, another mouse Y box protein. Polysome analysis demonstrates MSY4 is associated with mRNPs, consistent with MSY4 having a role in storing
Algorithms designed to identify canonical yeast prions predict that around 250 human proteins, including several RNA-binding proteins associated with neurodegenerative disease, harbour a distinctive prion-like domain (PrLD) enriched in uncharged polar amino acids and glycine. PrLDs in RNA-binding proteins are essential for the assembly of ribonucleoprotein granules. However, the interplay between human PrLD function and disease is not understood. Here we define pathogenic mutations in PrLDs of heterogeneous nuclear ribonucleoproteins (hnRNPs) A2B1 and A1 in families with inherited degeneration affecting muscle, brain, motor neuron and bone, and in one case of familial amyotrophic lateral sclerosis. Wild-type hnRNPA2 (the most abundant isoform of hnRNPA2B1) and hnRNPA1 show an intrinsic tendency to assemble into self-seeding fibrils, which is exacerbated by the disease mutations. Indeed, the pathogenic mutations strengthen a steric zipper motif in the PrLD, which accelerates the formation of self
ZBP1 (zipcode binding proteins 1) is an RNA-binding protein involved in many posttranscriptional processes such as RNA localization RNA stability and translational control. both cell adhesion and transcription specifically binds to the ZBP1 promoter via a conserved β-catenin/TCF4 response element and activates its gene expression. ZBP1 activation is also closely correlated with nuclear translocation of β-catenin in human breast tumors. We further demonstrate feedback regulation by finding that ZBP1 physically associates with β-catenin mRNA in vivo and increases its stability. These experiments suggest that in breast Pomalidomide cancer cells the expression of ZBP1 and the expression of β-catenin are coordinately regulated. β-Catenin mediates the transcription of the ZBP1 gene while ZBP1 promotes the stability of β-catenin mRNA. ZBP1 (zipcode binding protein 1) belongs to a conserved family of RNA-binding proteins that contain four hnRNP K (KH) domains and Pomalidomide two RNA recognition ...
Understanding how biomolecules interact is a major task of systems biology. To model protein-nucleic acid interactions, it is important to identify the DNA or RNA-binding residues in proteins. Protein sequence features, including the biochemical property of amino acids and evolutionary information in terms of position-specific scoring matrix (PSSM), have been used for DNA or RNA-binding site prediction. However, PSSM is rather designed for PSI-BLAST searches, and it may not contain all the evolutionary information for modelling DNA or RNA-binding sites in protein sequences. In the present study, several new descriptors of evolutionary information have been developed and evaluated for sequence-based prediction of DNA and RNA-binding residues using support vector machines (SVMs). The new descriptors were shown to improve classifier performance. Interestingly, the best classifiers were obtained by combining the new descriptors and PSSM, suggesting that they captured different aspects of evolutionary
RNA-protein interactions are pivotal in fundamental cellular processes such as translation, mRNA processing, early development, and infection by RNA viruses. However, in spite of the central importance of these interactions, few approaches are available to analyze them rapidly in vivo. We describe a yeast genetic method to detect and analyze RNA-protein interactions in which the binding of a bifunctional RNA to each of two hybrid proteins activates transcription of a reporter gene in vivo. We demonstrate that this three-hybrid system enables the rapid, phenotypic detection of specific RNA-protein interactions. As examples, we use the binding of the iron regulatory protein 1 (IRP1) to the iron response element (IRE), and of HIV trans-activator protein (Tat) to the HIV trans-activation response element (TAR) RNA sequence. The three-hybrid assay we describe relies only on the physical properties of the RNA and protein, and not on their natural biological activities; as a result, it may have broad ...
RNA-binding proteins regulate a number of cellular processes, including synthesis, folding, translocation, assembly and clearance of RNAs. Recent studies have reported that an unexpectedly large number of proteins are able to interact with RNA, but partners of many RNA-binding proteins are still uncharacterized.
Understanding interactions between proteins and RNA is key to deciphering the mechanisms of many important biological processes. Here we describe RNABindR, a web-based server that identifies and displays RNA-binding residues in known protein-RNA complexes and predicts RNA-binding residues in proteins of unknown structure. RNABindR uses a distance cutoff to identify which amino acids contact RNA in solved complex structures (from the Protein Data Bank) and provides a labeled amino acid sequence and a Jmol graphical viewer in which RNA-binding residues are displayed in the context of the three-dimensional structure. Alternatively, RNABindR can use a Naive Bayes classifier trained on a non-redundant set of protein-RNA complexes from the PDB to predict which amino acids in a protein sequence of unknown structure are most likely to bind RNA. RNABindR automatically displays high specificity and high sensitivity predictions of RNA-binding residues. RNABindR is freely available at http://bindr.gdcb.iastate
Sepsis represents uncontrolled inflammation due to an infection. Cold-inducible RNA-binding protein (CIRP) is a stress-induced damage-associated molecular pattern (DAMP). A subset of neutrophils expressing ICAM-1+ neutrophils was previously shown to produce high levels of reactive oxygen species. The role of CIRP for the development and function of ICAM-1+ neutrophils during sepsis is unknown. We hypothesize that CIRP induces ICAM-1 expression in neutrophils causing injury to the lungs during sepsis. Using a mouse model of cecal ligation and puncture (CLP)-induced sepsis, we found increased expression of CIRP and higher frequencies and numbers of ICAM-1+ neutrophils in the lungs ...
RNA-binding protein which may be involved in spermatogenesis. Required for sperm development, possibly by participating in pre-mRNA splicing in the testis.
Pentatricopeptide repeat (PPR) proteins are characterized by tandem repeats of a degenerate 35 amino acid motif [1]. Most of PPR proteins have roles in mitochondria or plastid. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [1,2]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [3,4,5]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see ,PDOC50005,) [1]. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organization [6,7]: ...
As published in the January 15th issue of G&D, Dr. Joel Richter s laboratory at UMASS Medical School has identified a critical role for the RINGO/Spy protein in the control of cytoplasmic polyadenylation. CPEB is a highly conserved, sequence-specific RNA-binding protein that modulates polyadenylation, and thereby mRNA translation. Dr. Richter and his graduate student, Kiran Padmanabhan, now show that CPEB phosphorylation (and subsequent activation) is regulated by RINGO/Spy in Xenopus oocytes. ...
The double-stranded RNA binding protein Staufen is required for the microtubule-dependent localization of bicoid and oskar mRNAs to opposite poles of the Drosophila oocyte and also mediates the actin-dependent localization of prospero mRNA during the asymmetric neuroblast divisions. The posterior localization of oskar mRNA requires Staufen RNA binding domain 2, whereas prospero mRNA localization mediated the binding of Miranda to RNA binding domain 5, suggesting that different Staufen domains couple mRNAs to distinct localization pathways. This study shows that the expression of Miranda during mid-oogenesis targets Staufen/oskar mRNA complexes to the anterior of the oocyte, resulting in bicaudal embryos that develop an abdomen and pole cells instead of the head and thorax. Anterior Miranda localization requires microtubules, rather than actin, and depends on the function of Exuperantia and Swallow, indicating that Miranda links Staufen/oskar mRNA complexes to the bicoid mRNA localization ...
We have characterized two RNA-binding proteins, of apparent molecular masses of approximately 40 and 35 kDa, which possess a single N-terminal RNA-recognition motif (RRM) followed by a C-terminal domain rich in serine-arginine dipeptides. Their primary structures resemble the single-RRM serine-arginine (SR) protein, SC35; however their functional effects are quite distinctive. The 40-kDa protein cannot complement SR protein-deficient HeLa cell S100 extract and showed a dominant negative effect in vitro against the authentic SR proteins, SF2/ASF and SC35. Interestingly, the 40- and 35-kDa proteins antagonize SR proteins and activate the most distal alternative 5 splice site of adenovirus E1A pre-mRNA in vivo, an activity that is similar to that characterized previously for the heterogeneous nuclear ribonucleoprotein particles A/B group of proteins. A series of recombinant chimeric proteins consisting of domains from these proteins and SC35 in various combinations showed that the RRM, but not the C
Fingerprint Dive into the research topics of RNA-binding protein RBM24 regulates p63 expression via mRNA stability. Together they form a unique fingerprint. ...
Alternative pre-mRNA splicing is a powerful mechanism that is exploited by higher eukaryotes to diversify their proteomes, and to differentially regulate the expression, function, and localization of mRNA and proteins. Pre-mRNA splicing is typically regulated by RNA-binding proteins that recognize cis-acting RNA elements, and either activate or repress splicing of adjacent exons in a temporal, and tissue specific, manner. Understanding how RNA-binding proteins control the splicing code is fundamental to understanding organismal development and disease. The SR proteins are a well-conserved class of RNA-binding proteins that have an essential role in the regulation of splice site selection, and have also been implicated as key regulators during other stages of RNA metabolism. The complexity of the RNA targets, and specificity of RNA binding location remains poorly understood for many members of the SR protein family. Here, we present a comprehensive study to elucidate how the SR proteins ...
RNA-binding proteins have been suggested to move in association with RNA as it leaves the nucleus. The NPL3 gene of the yeast Saccharomyces cerevisiae encodes in nuclear protein with consensus RNA-binding motifs and similarity to heterogeneous nuclear ribonucleoproteins and members of the S/R protein family. We show that although Npl3 is located in the nucleus, it can shuttle between nuclei in yeast heterokaryons. In contrast, other nucleus-targeted proteins do not leave the nucleus under similar conditions. Mutants missing the RNA-binding motifs or the N terminus are still capable of shuttling in and out of the nucleus. Npl3 mutants missing the C terminus fail to localize to the nucleus. Overproduction of Npl3 in wild-type cells shows cell growth. This toxicity depends on the presence of series of unique repeats in the N terminus and localization to the nucleus. We suggest that the properties of Npl3 are consistent with it being involved in export of RNAs from the nucleus. ...
The myeloid translocation gene (MTG) proteins are non-DNA-binding transcriptional regulators capable of interacting with chromatin modifying proteins. As a consequence of leukemia-associated chromosomal translocations, two of the MTG proteins, MTG8 and MTG16, are fused to the DNA-binding domain of AML1, a transcriptional activator crucial for hematopoiesis. The AML1-MTG fusion proteins, as the wild type MTGs, display four conserved homology regions (NHR1-4) related to the Drosophila nervy protein. Structural protein analyses led us to test the hypothesis that specific MTG domains may mediate RNA binding. By using an RNA-binding assay based on synthetic RNA homopolymers and a panel of MTG deletion mutants, here we show that all the MTG proteins can bind RNA. The RNA-binding properties can be traced to two regions: the Zinc finger domains in the NHR4, which mediate Zinc-dependent RNA binding, and a novel short basic region (SBR) upstream of the NHR2, which mediates Zinc-independent RNA binding. The two
RNA-binding proteins (RBPs) allow cells to carry out pre-RNA processing and post-transcriptional regulation of gene expression, and aberrations in RBP functions have been linked to many diseases, including neurological disorders and cancer. Human cells encode thousands of RNA-binding proteins with u …
TY - JOUR. T1 - Nuclear-Import Receptors Reverse Aberrant Phase Transitions of RNA-Binding Proteins with Prion-like Domains. AU - Guo, Lin. AU - Kim, Hong Joo. AU - Wang, Hejia. AU - Monaghan, John. AU - Freyermuth, Fernande. AU - Sung, Julie C.. AU - ODonovan, Kevin. AU - Fare, Charlotte M.. AU - Diaz, Zamia. AU - Singh, Nikita. AU - Zhang, Zi Chao. AU - Coughlin, Maura. AU - Sweeny, Elizabeth A.. AU - DeSantis, Morgan E.. AU - Jackrel, Meredith E.. AU - Rodell, Christopher B.. AU - Burdick, Jason A.. AU - King, Oliver D.. AU - Gitler, Aaron D.. AU - Lagier-Tourenne, Clotilde. AU - Pandey, Udai Bhan. AU - Chook, Yuh Min. AU - Taylor, J. Paul. AU - Shorter, James. PY - 2018/4/19. Y1 - 2018/4/19. N2 - RNA-binding proteins (RBPs) with prion-like domains (PrLDs) phase transition to functional liquids, which can mature into aberrant hydrogels composed of pathological fibrils that underpin fatal neurodegenerative disorders. Several nuclear RBPs with PrLDs, including TDP-43, FUS, hnRNPA1, and ...
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Signaling-protein mRNAs tend to have long untranslated regions (UTRs) containing binding sites for RNA-binding proteins regulating gene expression. Here we show that a PUF-family RNA-binding protein, Mpt5, represses the yeast MAP-kinase pathway controlling differentiation to the filamentous form. Mpt5 represses the protein levels of two pathway components, the Ste7 MAP-kinase kinase and the Tec1 transcriptional activator, and negatively regulates the kinase activity of the Kss1 MAP kinase. Moreover, Mpt5 specifically inhibits the output of the pathway in the absence of stimuli, and thereby prevents inappropriate cell differentiation. The results provide an example of what may be a genome-scale level of regulation at the interface of signaling networks and protein-RNA binding networks.
Shop Nuclear polyadenylated RNA-binding protein ELISA Kit, Recombinant Protein and Nuclear polyadenylated RNA-binding protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
Allows to analyse binding sites of RNA-binding proteins. CLIPZ is a database and an analysis environment which supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins to identify the binding sites of these proteins. The software allows users to upload their own sequence data sets while being able to limit the access to these data to specific users.
Fingerprint Dive into the research topics of Splicing of the Drosophila Sex-lethal early transcripts involves exon skipping that is independent of Sex-lethal protein. Together they form a unique fingerprint. ...
Sigma-Aldrich offers abstracts and full-text articles by [Philip J Uren, Dat T Vo, Patricia Rosa de Araujo, Rebecca Pötschke, Suzanne C Burns, Emad Bahrami-Samani, Mei Qiao, Raquel de Sousa Abreu, Helder I Nakaya, Bruna R Correa, Caspar Kühnöl, Jernej Ule, Jennifer L Martindale, Kotb Abdelmohsen, Myriam Gorospe, Andrew D Smith, Luiz O F Penalva].
Mai S, et al. Global regulation of alternative RNA splicing by the SR-rich protein RBM39. Biochim Biophys Acta. 2016 Aug;1859(8):1014-24. (IF=5.373). ...
mRNA stability is modulated by elements in the mRNA transcript and their cognate RNA binding proteins. Poly(U) binding protein 1 (Pub1) is a cytoplasmic Saccharomyces cerevisiae mRNA binding protein that stabilizes transcripts containing AU-rich elements (AREs) or stabilizer elements (STEs). In a yeast two-hybrid screen, we identified nuclear poly(A) binding protein 2 (Nab2) as being a Pub1-interacting protein. Nab2 is an essential nucleocytoplasmic shuttling mRNA binding protein that regulates poly(A) tail length and mRNA export. The interaction between Pub1 and Nab2 was confirmed by copurification and in vitro binding assays. The interaction is mediated by the Nab2 zinc finger domain. Analysis of the functional link between these proteins reveals that Nab2, like Pub1, can modulate the stability of specific mRNA transcripts. The half-life of the RPS16B transcript, an ARE-like sequence-containing Pub1 target, is decreased in both nab2-1 and nab2-67 mutants. In contrast, GCN4, an STE-containing ...
Fingerprint Dive into the research topics of Regulation of tau RNA maturation by thyroid hormone is mediated by the neural RNA-binding protein musashi-1. Together they form a unique fingerprint. ...
Transcription factors (TFs) are well-established key factors orchestrating gene transcription, and RNA-binding proteins (RBPs) are mainly thought to participate in post-transcriptional control of gene. In fact, these two steps are functionally coupled, offering a possibility for reciprocal communications between transcription and regulatory RNAs and RBPs. Recently, a series of exploratory studies, utilizing functional genomic strategies, have revealed that RBPs are prevalently involved in transcription control genome-wide through their interactions with chromatin. Here, we present a refined census of RBPs to grope for such an emerging role and discuss the global view of RBP-chromatin interactions and their functional diversities in transcription regulation. ...
Sigma-Aldrich offers abstracts and full-text articles by [Meghdad Yeganeh, Ehsan Seyedjafari, Farnaz Akbari Kamrani, Nasser Ghaemi].
The expression profile of a panel of RNA-binding proteins (heterogeneous ribonucleoprotein (hnRNP) A1, hnRNP C1/C2, hnRNP H, hnRNP I, ASF/SF2, SR proteins, HuR and U2AF(65)) and markers of differentiation, proliferation and neoplasia (cytokeratin (CK) 13, CK-14, proliferating cell nuclear antigen (PCNA), Syndecan-1 and p16INK4a) were analyzed in 50 formalin fixed paraffin embedded cervical tissues using immunohistochemistry. The samples included histologically normal cervical epithelium, human papillomavirus (HPV) induced low-grade and high-grade pre-malignant lesions and cervical cancers. All samples were tested for HPV DNA using nested PCR. Forty-nine of the 50 tissue samples tested positive for HPV, 27 tissue samples (54%) were HPV-16 positive and 4 samples (8%) were HPV-18 positive. The immunohistochemistry results detected different expression levels of the various proteins in basal epithelial cells in histologically normal epithelium followed by an increase in expression in the ...
RNA-binding proteins (RBPs) are effectors and regulators of posttranscriptional gene regulation (PTGR). RBPs regulate stability, maturation, and turnover of all RNAs, often binding thousands of target
RNA in cells is always associated with RNA-binding proteins that regulate all aspects of RNA metabolism including RNA splicing, export from the nucleus, RNA localization, mRNA turn-over as well as translation. Given their diverse functions, cells express a variety of RNA-binding proteins, which play important roles in the pathologies of a number of diseases. In this review we focus on the effect of alcohol on different RNA-binding proteins and their possible contribution to alcohol-related disorders, and discuss the role of these proteins in the development of neurological diseases and cancer. We further discuss the conventional methods and newer techniques that are employed to identify RNA-binding proteins.
Regulation of gene expression, protein synthesis, replication and assembly of many viruses involve RNA-protein interactions. Although some successful computational tools have been reported to recognize RNA binding sites in proteins, the problem of specificity remains poorly investigated. After the nucleotide base composition, the dinucleotide is the smallest unit of RNA sequence information and many RNA-binding proteins simply bind to regions enriched in one dinucleotide. Interaction preferences of protein subsequences and dinucleotides can be inferred from protein-RNA complex structures, enabling a training-based prediction approach. We analyzed basic statistics of amino acid-dinucleotide contacts in protein-RNA complexes and found their pairing preferences could be identified. Using a standard approach to represent protein subsequences by their evolutionary profile, we trained neural networks to predict multiclass target vectors corresponding to 16 possible contacting dinucleotide subsequences. In the
In addition to DNA, gametes contribute epigenetic information in the form of histones and non-coding RNA. Epigenetic programs often respond to stressful environmental conditions and provide a heritable history of ancestral stress that allows for adaptation and propagation of the species. In the nematode C. elegans, defective epigenetic transmission often manifests as progressive germline mortality. We previously isolated sup-46 in a screen for suppressors of the hexosamine pathway gene mutant, gna-2(qa705). In this study, we examine the role of SUP-46 in stress resistance and progressive germline mortality. We identified SUP-46 as an HNRNPM family RNA-binding protein, and uncovered a highly novel role for SUP-46 in preventing paternally-mediated progressive germline mortality following mating. Proximity biotinylation profiling of human homologs (HNRNPM, MYEF2) identified proteins of ribonucleoprotein complexes previously shown to contain non-coding RNA. Like HNRNPM and MYEF2, SUP-46 was associated with
Small RNAs, 5 UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence. FEMS Microbiol Rev. 2015 May;39(3):331-349 Authors: Oliva G, Sahr T, Buchrieser C Abstract Sequencing-based studies have illuminated increased transcriptional complexity within the genome structure of bacteria and have resulted in the identification of many small regulatory RNAs (sRNA) and…
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TY - JOUR. T1 - Mammalian ELAV-like neuronal RNA-binding proteins HuB and HuC promote neuronal development in both the central and the peripheral nervous systems. AU - Akamatsu, Wado. AU - Okano, Hirotaka J.. AU - Osumi, Noriko. AU - Inoue, Takayoshi. AU - Nakamura, Shun. AU - Sakakibara, Shin Ichi. AU - Miura, Masayuki. AU - Matsuo, Nobutake. AU - Darnell, Robert B.. AU - Okano, Hideyuki. PY - 1999/8/17. Y1 - 1999/8/17. N2 - Hu proteins are mammalian embryonic lethal abnormal visual system (ELAV)-like neuronal RNA-binding proteins that contain three RNA recognition motifs. Although Drosophila ELAV is required for the correct differentiation and survival of neurons, the roles played by the Hu genes in the mammalian nervous system remain largely unknown. To explore the in vivo functions of mouse Hu proteins, we overexpressed them in rat pheochromocytoma PC12 cells, where they induced neuronal phenotype in the absence of nerve growth factor. We have characterized the functions of various forms of ...
Nuclear RNA processing is a critical stage in eukaryotic gene expression, and is controlled in part by the expression and concentration of nuclear RNA-binding proteins. Different nuclear RNA-binding proteins are differentially expressed in different cells, helping the spliceosome to decode pre-mRNAs into alternatively spliced mRNAs. Recent post-genomic technology has exposed the complexity of nuclear RNA processing, and is starting to reveal the mechanisms and rules through which networks of RNA-binding proteins can regulate multiple parallel pathways. Identification of multiple parallel processing pathways regulated by nuclear RNA-binding proteins is leading to a systems-wide understanding of the rules and consequences of alternative nuclear RNA processing.. ...
TY - JOUR. T1 - Interaction of RNA-binding proteins HuR and AUF1 with the human ATF3 mRNA 3′-untranslated region regulates its amino acid limitation-induced stabilization. AU - Pan, Yuan Xiang. AU - Chen, Hong. AU - Kilberg, Michael S.. PY - 2005/10/14. Y1 - 2005/10/14. N2 - ATF3 expression is induced in cells exposed to a variety of stress conditions, including nutrient limitation. Here we demonstrated that the mechanism by which the ATF3 mRNA content is increased following amino acid limitation of human HepG2 hepatoma cells is mRNA stabilization. Analysis of ATF3 mRNA turnover revealed that the half-life was increased from about 1 h in control cells to greater than 8 h in the histidine-deprived state, demonstrating mRNA stabilization in response to nutrient deprivation. Treatment of HepG2 cells with thapsigargin, which causes endoplasmic reticulum stress, also increased the half-life of ATF3 mRNA. HuR is an RNA-binding protein that regulates both the stability and cytoplasmic/nuclear ...
TY - JOUR. T1 - Antitumor effects of EMAP II against pancreatic cancer through inhibition of fibronectin-dependent proliferation. AU - Schwarz, Roderich E.. AU - Awasthi, Niranjan. AU - Konduri, Srivani. AU - Caldwell, Lauren. AU - Cafasso, Danielle. AU - Schwarz, Margaret A.. N1 - Copyright: Copyright 2017 Elsevier B.V., All rights reserved.. PY - 2010/4/15. Y1 - 2010/4/15. N2 - Pancreatic ductal adenocarcinoma (PDAC) is highly resistant to conventional chemotherapy. The presence of both cellular and stromal fibronectin (FN) and its interaction with integrins is necessary for PDAC progression. We tested the efficacy of endothelial monocyte-activating polypeptide II (EMAP II) to inhibit PDAC progression and its ability to interfere with FN-integrin angiogenesis signaling. In heterotopic PDAC tumors EMAP II caused a significant reduction (,65%) in tumor growth, accompanied by a ,50% and 44% decrease in microvessel density and proliferative activity, respectively. EMAP II therapy caused a 62% and ...
Elucidation of the interaction of proteins with different molecules is of significance in the understanding of cellular processes. Computational methods have been developed for the prediction of protein-protein interactions. But insufficient attention has been paid to the prediction of protein-RNA interactions, which play central roles in regulating gene expression and certain RNA-mediated enzymatic processes. This work explored the use of a machine learning method, support vector machines (SVM), for the prediction of RNA-binding proteins directly from their primary sequence. Based on the knowledge of known RNA-binding and non-RNA-binding proteins, an SVM system was trained to recognize RNA-binding proteins. A total of 4011 RNA-binding and 9781 non-RNA-binding proteins was used to train and test the SVM classification system, and an independent set of 447 RNA-binding and 4881 non-RNA-binding proteins was used to evaluate the classification accuracy. Testing results using this independent ...
Mammalian gene expression patterns change profoundly in response to low oxygen levels. These changes in gene expression programs are strongly influenced by post-transcriptional mechanisms mediated by mRNA-binding factors: RNA-binding proteins (RBPs) and microRNAs (miRNAs). Here, we review the RBPs and miRNAs that modulate mRNA turnover and translation in response to hypoxic challenge. RBPs such as HuR (human antigen R), PTB (polypyrimidine tract-binding protein), heterogeneous nuclear ribonucleoproteins (hnRNPs), tristetraprolin, nucleolin, iron-response element binding proteins (IRPs), and cytoplasmic polyadenylation-element-binding proteins (CPEBs), selectively bind to numerous hypoxia-regulated transcripts and play a major role in establishing hypoxic gene expression patterns. MiRNAs including miR-210, miR-373, and miR-21 associate with hypoxia-regulated transcripts and further modulate the levels of the encoded proteins to implement the hypoxic gene expression profile. We discuss the potent
Methionyl-tRNA synthetase (MetRS) belongs to the family of 20 enzymes essential for protein biosynthesis. It links covalently methionine with its cognate tRNA. Crystal structures solved for bacterial MetRSs have given a number of interesting insights into enzyme architecture and methionylation catalysis. A comparison of sequences of MetRSs belonging to all kingdoms of life, as well as numerous biochemical and genetic studies have revealed the presence of various additional domains appended to the catalytic core of synthetase. They are responsible for interactions with tRNA and proteins. Tertiary structure of C-terminal tRNA-binding appendices can be deduced from those determined for their homologues: tRNA binding protein 111 and endothelial monocyte-activating polypeptide II. Contacts between MetRS and other proteins could be mediated not only by noncatalytic peptides but also by structural elements present in the catalytic core, e.g. Arg-Gly-Asp (RGD) motifs. Additional activities involve MetRS ...
TY - JOUR. T1 - Hrb27C, Sqd and Otu cooperatively regulate gurken RNA localization and mediate nurse cell chromosome dispersion in Drosophila oogenesis. AU - Goodrich, Jennifer S.. AU - Clouse, K. Nicole. AU - Schüpbach, Trudi. PY - 2004/5. Y1 - 2004/5. N2 - Heterogeneous nuclear ribonucleoproteins, hnRNPs, are RNA-binding proteins that play crucial roles in controlling gene expression. In Drosophila oogenesis, the hnRNP Squid (Sqd) functions in the localization and translational regulation of gurken (grk) mRNA. We show that Sqd interacts with Hrb27C, an hnRNP previously implicated in splicing. Like sqd, hrb27C mutants lay eggs with dorsoventral defects and Hrb27C can directly bind to grk RNA. Our data demonstrate a novel role for Hrb27C in promoting grk localization. We also observe a direct physical interaction between Hrb27C and Ovarian tumor (Otu), a cytoplasmic protein implicated in RNA localization. We find that some otu alleles produce dorsalized eggs and it appears that Otu cooperates ...
TY - JOUR. T1 - Conserved RNA-binding specificity of polycomb repressive complex 2 is achieved by dispersed amino acid patches in EZH2. AU - Long, Yicheng. AU - Bolanos, Ben. AU - Gong, Lihu. AU - Liu, Wei. AU - Goodrich, Karen J.. AU - Yang, Xin. AU - Chen, Siming. AU - Gooding, Anne R.. AU - Maegley, Karen A.. AU - Gajiwala, Ketan S.. AU - Brooun, Alexei. AU - Cech, Thomas R.. AU - Liu, Xin. N1 - Funding Information: We thank members of the Cech lab, Oncology Structural Biology and Protein Science group, and the Liu lab for useful conversations. We also thank Daniel T Youmans for technical advice and reagents for the RNA immunoprecipitation experiments. TRC is an investigator of the HHMI, which supported this research. This research was supported by Welch Foundation research grant I-1790, CPRIT research grant R1119, Rita Allen Foundation research grant, UT Southwestern Medical Center Endowed Scholar fund, and NIH grants GM114576 and GM121662 to XL XL is a W W Caruth, Jr. Scholar in Biomedical ...
TY - JOUR. T1 - Xenopus Staufen is a component of a ribonucleoprotein complex containing Vg1 RNA and kinesin. AU - Yoon, Young J.. AU - Mowry, Kimberly L.. PY - 2004/7. Y1 - 2004/7. N2 - RNA localization is a key mechanism for generating cell and developmental polarity in a wide variety of organisms. We have performed studies to investigate a role for the Xenopus homolog of the double-stranded RNA-binding protein, Staufen, in RNA localization during oogenesis. We have found that Xenopus Staufen (XStau) is present in a ribonucleoprotein complex, and associates with both a kinesin motor protein and vegetally localized RNAs Vg1 and VegT. A functional role for XStau was revealed through expression of a dominant-negative version that blocks localization of Vg1 RNA in vivo. Our results suggest a central role for XStau in RNA localization in Xenopus oocytes, and provide evidence that Staufen is a conserved link between specific mRNAs and the RNA localization machinery.. AB - RNA localization is a key ...
The mouse cytoplasmic polyadenylation element-binding protein 3 (CPEB3) is a translational regulator implicated in long-term memory maintenance. Invertebrate orthologs of CPEB3 in Aplysia and Drosophila are functional prions that are physiologically active in the aggregated state. To determine if this principle applies to the mammalian CPEB3, we expressed it in yeast and found that it forms heritable aggregates that are the hallmark of known prions. In addition, we confirm in the mouse the importance of CPEB3s prion formation for CPEB3 function. Interestingly, deletion analysis of the CPEB3 prion domain uncovered a tripartite organization: two aggregation-promoting domains surround a regulatory module that affects interaction with the actin cytoskeleton. In all, our data provide direct evidence that CPEB3 is a functional prion in the mammalian brain and underline the potential importance of an actin/CPEB3 feedback loop for the synaptic plasticity underlying the persistence of long-term memory ...
Co-Coordinator , Professor, Dept. of Molecular Genetics & Microbiology , [email protected] Maurice Swanson is the co-coordinator of the Genetics & genomics doctoral program, and a professor in the department of molecular genetics & microbiology in the College of Medicine. Swanson works with incoming and current students, guiding them from the application process and through the doctoral program.. Swanson received his PhD from the University of California at Berkeley, followed by a postdoctoral fellowship at Northwestern University, where he studied the functions of nuclear and cytoplasmic RNA-binding proteins in RNA processing and mRNA translation. His current research is focused on the functions of repetitive DNA, particularly the roles of unstable microsatellites in RNA-mediated neurological and neuromuscular diseases.. ...
Mitochondrial RNA-binding proteins, molecular model. This complex consists of two mitochondrial RNA-binding proteins MRP1 and MRP2. These act together to bind to RNA (ribonucleic acid). Here, they here form a heteromeric complex, specifically a heterotetramer, with fourfold symmetry. These two proteins are from the protozoan Trypanosoma brucei. - Stock Image C015/4586
Mitochondrial RNA-binding proteins, molecular model. This complex consists of two mitochondrial RNA-binding proteins MRP1 and MRP2. These act together to bind to RNA (ribonucleic acid). Here, they here form a heteromeric complex, specifically a heterotetramer, with fourfold symmetry. These two proteins are from the protozoan Trypanosoma brucei. - Stock Image C015/4007
Project C1: The role of selected RNA-binding proteins and small RNAs in bacterial pathogenicity Monika Helm studied biochemistry at the Martin-Luther-University Halle-Wittenberg (2009-2014). As a PhD student Monika investigates potential roles of selected small RNAs (sRNAs) and putative RNA-binding proteins in the virulence of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv). Although a number of small RNAs were recently discovered in Xcv and virulence functions have been demonstrated for two of them, the targets of the other sRNAs are not known. Furthermore, the involvement of RNA-binding proteins in regulation of small RNA activity in Xcv is not well studied yet. Therefore, Monika aims at the identification and characterization of novel small RNA-binding proteins.. Supervisor: Prof. Ulla Bonas. Contact:. phone: 0345-5526296. eMail: monika.arnold(at) ...
PUFs are RNA binding proteins that promote mRNA deadenylation and decay and inhibit translation. Yeast Puf5 is the prototype for studying PUF-dependent gene repression. Puf5 binds to the Pop2 subunit of the Ccr4-Pop2-NOT mRNA deadenylase, recruiting the deadenylase and associated translational repressors to mRNAs. Here we used yeast genetics to show that Puf5 has additional roles in vivo that do not require Pop2. Deletion of PUF5 caused increased sensitivity to DNA replication stress in cells lacking Pop2, as well as in cells mutated for two activities recruited to mRNAs by the Puf5-Pop2 interaction, the deadenylase Ccr4 and the translational repressor Dhh1. A functional Puf5 RNA binding domain was required, and Puf5 cytoplasmic localisation was sufficient for resistance to replication stress, indicating posttranscriptional gene expression control is involved. In contrast to DNA replication stress, in response to the cell wall integrity pathway activator caffeine, PUF5 and POP2 acted in the same genetic
Polypyrimidine Tract Binding Protein (PTB) is an intensely studied RNA binding protein involved in several post-transcriptional regulatory events of gene expression. Initially described as a pre-mRNA splicing regulator, PTB is now widely accepted as a multifunctional protein shuttling between nucleus and cytoplasm. Accordingly, PTB can interact with selected RNA targets, structural elements and proteins. There is increasing evidence that PTB and its paralog PTBP2 play a major role as repressors of alternatively spliced exons, whose transcription is tissue-regulated. In addition to alternative splicing, PTB is involved in almost all steps of mRNA metabolism, including polyadenylation, mRNA stability and initiation of protein translation. Furthermore, it is well established that PTB recruitment in internal ribosome entry site (IRES) activates the translation of picornaviral and cellular proteins. Detailed studies of the structural properties of PTB have contributed to our understanding of the mechanism of
Human RNA-binding protein (HuR), a ubiquitously expressed member of the Hu protein family, plays an important role in mRNA degradation and has been implicated as a key post-transcriptional regulator. HuR contains three RNA-recognition motif (RRM) domains. The two N-terminal tandem RRM domains can se …
The discovery that repeat expansions in C9orf72 gene has led to many exciting discoveries in the past few years. This expansion causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) and is responsible for the majority of ALS and FTD cases of European ancestry. Three, not mutually exclusive pathological mechanisms have been proposed: i) Formation of RNA foci sequestering specific RNA-binding proteins and impairing their normal function; ii) Repeat-associated non-AUG-initiated (RAN) translation of RNA repeats into toxic dipeptide repeat proteins (DPRs) and iii) haploinsufficiency resulting in reduced levels of the C9orf72 protein contributing to pathogenesis.The pathological mechanisms of C9orf72-linked disease are a very active and timely research field and many original papers and reviews are regularly published on this subject. Therefore, the goal of this Research Topic is to address the most recent progress in unraveling molecular mechanisms of C9orf72 neurodegeneration.
Heme oxygenase-1 (HO-1) is an inducible rate-controlling enzyme of heme catabolism. The cytoprotective function of HO-1 activity has been verified in multiple studies, and together with its by-products is considered a key component of the cellular stress response. The transcriptional induction of HO-1 has been largely studied in response to multiple forms of stressful stimuli but our understanding of HO-1 post-transcriptional control mechanisms in neuronal cells is currently lacking. In the present report we show the involvement of the RNA-binding proteins ELAV in the regulation of HO-1 gene expression. Our study demonstrates a specific binding between HO-1 mRNA and ELAV proteins, accompanied by an increased expression of HO-1 at protein level, in a human neuroblastoma cell line treated with hemin. Clarifying the induction of HO-1 expression at post-transcriptional level may open therapeutic perspectives for treatments associated with the modulation of HO-1 expression.. ...
An RNA-binding protein that is overproduced in ovarian cancer may pres...Researchers in the UIC College of Pharmacy found that interfering with... In a previous study we observed that human ovarian tumors overexpres...In the new study Beck and research assistant professor Xiaolong He sh...The research has been published in the online version of the journal O...,RNA,splicing,factor,implicated,in,ovarian,tumor,cell,growth,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
J.C. Schöning, et al., Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis, Nucleic Acids Research, vol. 36, 2008, pp. 6977-6987 ...
RNA-binding proteins interact with specific RNA molecules to regulate important cellular processes. It is therefore necessary to identify the RNA interaction partners in order to understand the precise functions of such proteins. Protein-RNA interactions are typically characterized using in vivo and in vitro experiments but these may not detect all binding partners. Therefore, computational methods that capture the protein-dependent nature of such binding interactions could help to predict potential binding partners in silico. We have developed three methods to predict whether an RNA can interact with a particular RNA-binding protein using support vector machines and different features based on the sequence (the Oli method), the motif score (the OliMo method) and the secondary structure (the OliMoSS method). We applied these approaches to different experimentally-derived datasets and compared the predictions with RNAcontext and RPISeq. Oli outperformed OliMoSS and RPISeq, confirming our protein-specific
Sense and antisense transcripts of the repeat accumulate in ubiquitous small nuclear, and occasionally cytoplasmic, RNA foci. Many (G4C2) n -binding proteins have been identified that are partially sequestered by the repeat RNA. Several of the trapped RNA-binding proteins are involved in alternative splicing and splicing abnormalities have been reported in C9orf72 patients [22, 25]. However, a sophisticated study on 63 C9orf72 cases shows no correlation of sense and antisense foci with neurodegeneration or clinical parameters [6], although antisense foci have been linked to TDP-43 pathology by others [5].. Repeat-associated non-ATG (RAN) translation of both sense and antisense repeat transcripts in all reading frames generates five co-aggregating dipeptide repeat (DPR) proteins: poly-GA/GP/GR from the sense transcript and poly-GP/PA/PR from the antisense transcript. The sense-strand derived DPRs are abundant throughout the neocortex, hippocampus, thalamus and cerebellum, but scarce in brain stem ...
The selective expression of Musashi1 in stem cells or immature cells of these tissues led us to speculate that it plays a role in keeping these cells in an undifferentiated state during post-transcriptional gene regulation. We sought to identify its target RNA by using a strategy similar to that used in the study of Drosophila Musashi. By in vitro selection, we determined that the consensus ligand RNA sequence for mammalian Musashi1 is G/AU2-3(AGU). We then explored candidates for the in vivo Musashi1 target gene on the basis of the results of in vitro selection experiments as well as expression patterns and functions. We speculated that mRNAs of genes regulating neural differentiation (either positively or negatively) would be downstream targets of Musashi1 since Musashi1 is preferentially expressed in undifferentiated neuronal progenitor cells.. One of the in vivo targets of Musashi1 is m-Numb mRNA, the 3′ UTR of which has a Musashi1-binding site ( Imai et al., 2001). The m-Numb and Musashi1 ...
RNA-Binding Motif Protein 17 or Splicing factor 45 is encoded by the gene RBM17. RBM17 is a component of the spliceosome complex and displays catalytic activity during mRNA splicing. RBM17 is involved in alternative splicing, resulting in different isoforms of a gene. RBM is also thought to play a role in DNA repair (Red: Chaouki et al 2006) RBM17 is widely expressed in the nucleus and important for development. Diseases associated with this gene include sickle cell anemia and forms of Ataxia 1 ...
File:OlivasLab-Pufaction.tiff Cells respond to environmental signals and stresses by transcriptional regulation of response genes, as well as activation of more rapid post-transcriptional regulatory pathways. Modulation of mRNA degradation and translation rates is an efficient method to rapidly alter protein production in response to cellular changes. The Puf family of eukaryotic RNA-binding proteins control critical decisions in cell development and differentiation by regulating the degradation and translation of target mRNAs through interactions with 3 untranslated regions (UTRs). Pufs are also involved in cellular stress responses. Research in our lab utilizes the yeast model system Saccharomyces cerevisiae to determine how Puf proteins integrate environmental signals to alter their regulation of mRNA metabolism. For example, we have demonstrated that Puf3p responds to environmental carbon source signals to regulate the decay of nuclear-encoded transcripts that code for mitochondrial ...
This enzyme is activated during Fas-mediated apoptosis. Following Fas ligation, the enzyme, which is constitutively phosphorylated, is dephosphorylated, and it is the dephosphorylated form that causes phosphorylation of TIA-1, a nuclear RNA-binding protein. Phosphorylation of TIA-1 precedes the onset of DNA fragmentation ...
RBMY2EP (RNA binding motif protein Y-linked family 2 member E, pseudogene), Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.
All of the work and power in the methodology is on the sample prep side, so hopefully you have someone great who does that for you! They validate the assay by using a human cancer cell line and identify about 1,000 RNA binding sites -- many previously characterized, and a bunch of new ones ...
Disruption of a mitochondrial RNA-binding protein gene results in decreased cytochrome b expression and a marked reduction in ubiquinol-cytochrome c reductase activity in mouse heart mitochondria ...
PMID: 14559993. SRrp86 is a unique member of the SR protein superfamily containing one RNA recognition motif and two serine-arginine (SR)-rich domains separated by an unusual glutamic acid-lysine (EK)-rich region. Previously, we showed that SRrp86 could regulate alternative splicing by both positively and negatively modulating the activity of other SR proteins and that the unique EK domain could inhibit both constitutive and alternative splicing. These functions were most consistent with the model in which SRrp86 functions by interacting with and thereby modulating the activity of target proteins. To identify the specific proteins that interact with SRrp86, we used a yeast two-hybrid library screen and immunoprecipitation coupled to mass spectrometry. We show that SRrp86 interacts with all of the core SR proteins, as well as a subset of other splicing regulatory proteins, including SAF-B, hnRNP G, YB-1, and p72. In contrast to previous results that showed activation of SRp20 by SRrp86, we now ...
We describe a novel RNA binding protein, Y14, a predominantly nuclear nucleocytoplasmic shuttling protein. Interestingly, Y14 associates preferentially with mRNAs produced by splicing but not with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Y14 associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs. Splicing of a single intron is sufficient for Y14 association. Y14-containing nuclear complexes are different from general hnRNP complexes. They contain hnRNP proteins and several unique proteins including the mRNA export factor TAP. Thus, Y14 defines novel intermediates in the pathway of gene expression, postsplicing nuclear preexport mRNPs, and newly exported cytoplasmic mRNPs, whose composition is established by splicing. These findings suggest that pre-mRNA splicing imprints mRNA with a unique set of proteins that persists in the cytoplasm and thereby communicates the history of the transcript ...
FMR1 is an RNA-binding protein that is either absent or mutated in patients affected by the fragile X syndrome, the most common inherited cause of mental retardation in humans. Sequence analysis of the FMR1 protein has suggested that RNA binding is related to the presence of two K-homologous (KH) modules and an RGG box. However, no attempt has been so far made to map the RNA-binding sites along the protein sequence and to identify possible differential RNA-sequence specificity. In the present article, we describe work done to dissect FMR1 into regions with structurally and functionally distinct properties. A semirational approach was followed to identify four regions: an N-terminal stretch of 200 amino acids, the two KH regions, and a C-terminal stretch. Each region was produced as a recombinant protein, purified, and probed for its state of folding by spectroscopical techniques. Circular dichroism and NMR spectra of the N-terminus show formation of secondary structure with a strong tendency to ...
1L3K: Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1.
The central dogma of biology describes the flow of genetic information from DNA to RNA to proteins. While RNA was originally believed to be a carrier of genetic information, subsequent work has shown something completely different: RNA is now known to have function independent of proteins, with a rich layer of regulatory networks. In fact, a large amount of the RNA present in a cell does not actually make proteins. This increased appreciation and understanding has led to many fascinating mechanistic insights into RNA and its role as a central player in cellular regulation and human disease.. Helping to facilitate RNA function are a large number of proteins that can bind to and regulate RNA. These RNA-binding proteins, or RBPs, number in the thousands and are made up of many different independent modular segments similar to a childs set of building blocks. In much a similar fashion, these blocks or domains provide nature with a way of mixing and matching different domains to generate new ...
Musashi Protein Powders and Supplements are well known for their Musashi Bulk, SLM, Creatine and Musashi protein bars. The Musashi brand produces supplements according to TGA standards of therapeutic goods which enables Musashi Supplements to meet world class nutrition standards. Musashi, Australias Trusted Performance Nutrition company was established in 1987. The business is named after Miyamoto Musashi, a Japanese swordsman famed for his duels and distinctive style as well as authoring The Book of Five Rings- a book on strategy, tactics, and philosophy.
TY - JOUR. T1 - Cyclin A2 is an RNA binding protein that controls Mre11 mRNA translation. AU - Kanakkanthara, Arun. AU - Jeganathan, Karthik B.. AU - Limzerwala, Jazeel F.. AU - Baker, Darren J.. AU - Hamada, Masakazu. AU - Nam, Hyun Ja. AU - Van Deursen, Willemijn H.. AU - Hamada, Naomi. AU - Naylor, Ryan M.. AU - Becker, Nicole A.. AU - Davies, Brian A.. AU - Van Ree, Janine H.. AU - Mer, Georges. AU - Shapiro, Virginia S.. AU - Maher, L. James. AU - Katzmann, David J.. AU - Van Deursen, Jan M.. N1 - Funding Information: We thank W. Zhou, M. Li, F. Jin, and X. Wang for assistance and D. Compton for providing photoactivatable GFP-tagged ?-tubulin. Supported by NIH grants CA126828 and CA168709 (J.M.v.D.) and CA166025 (L.J.M.). Publisher Copyright: © 2016, American Association for the Advancement of Science. All rights reserved.. PY - 2016/9/30. Y1 - 2016/9/30. N2 - Cyclin A2 activates the cyclin-dependent kinases Cdk1 and Cdk2 and is expressed at elevated levels from S phase until early ...
In a screen for RNA-binding proteins expressed during murine spermatogenesis, we have identified a cDNA that encodes a protein of 911 amino acids that contains two copies of the double-stranded RNA-binding ...
In a screen for RNA-binding proteins expressed during murine spermatogenesis, we have identified a cDNA that encodes a protein of 911 amino acids that contains two copies of the double-stranded RNA-binding ...
April 2015). "Systematic discovery of Xist RNA binding proteins". Cell. 161 (2): 404-16. doi:10.1016/j.cell.2015.03.025. PMC ... PRC2 binds the A-repeat (RepA) of Xist RNA directly and with very high affinity (dissociation constants of 10-100 nanomolar), ... Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT (October 2008). "Polycomb proteins targeted by a short repeat RNA to the mouse X ... February 2014). "Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy". Proceedings of ...
... one by mutations in the RNA binding protein while the other being an expansion of nucleotide repeats in the RNA. Another ... is mRNA with bound proteins. mRNA does not exist "naked" in vivo but is always bound by various proteins while being ... Later, the pre-mRNA is bound by the spliceosome containing exon and intron definition complexes and proteins and RNA that ... Neuronal RNP granules that are connected to RNA binding proteins show signs of causing neurodevelopment, neurodegeneration or ...
... also known as ataxin 2-binding protein 1 (A2BP1) or hexaribonucleotide-binding protein 1 (HRNBP1) or RNA binding protein, fox-1 ... Rbfox1 has an RNA recognition motif that is highly conserved among RNA-binding proteins. Rbfox1, and the related protein Rbfox2 ... A2BP1 ataxin 2-binding protein 1". CS1 maint: discouraged parameter (link) Jin, Y. (2003-02-17). "A vertebrate RNA-binding ... Shibata H, Huynh DP, Pulst SM (May 2000). "A novel protein with RNA-binding motifs interacts with ataxin-2". Human Molecular ...
Identification of novel Y RNA-binding proteins". European Journal of Biochemistry. 267 (9): 2778-89. doi:10.1046/j.1432- ... Tripartite motif-containing protein 21, also known as E3 ubiquitin-protein ligase TRIM21, is a protein that in humans is ... The TRIM motif includes three zinc-binding domains, a RING finger domain, a B-box type 1 and a B-box type 2 zinc finger, and a ... TRIM21 itself is not degraded in the proteasome unlike both the viral capsid and the bound antibody. TRIM21 is part of the ...
Tuschl, Thomas; Hafner, Markus; Gerstberger, Stefanie (December 2014). "A census of human RNA-binding proteins". Nature Reviews ... "N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions". Nature. 518 (7540): 560-564. doi: ... Ding researches RNA structure and post-transcriptional gene regulations. Ding's research on nucleic acid chemistry and RNA ... In particular her work on a high throughput method, Structure-seq to analyse one of the first two genome-wide in vivo RNA ...
PAR-CLIP: A method for identifying the binding sites of cellular RNA-binding proteins. RIP-Chip: Similar to ChIP-Seq, but does ... conjugated Tn5 bound to a protein of interest. Tn5 mediated cleavage produces a library of target DNA sites bound to a protein ... ChiRP-Seq: Measures RNA-bound DNA and proteins. ChIP-exo: Employs exonuclease treatment to achieve up to single base-pair ... It can be used to map global DNA binding sites precisely for any protein of interest. Currently, ChIP-Seq is the most common ...
PAR-CLIP: A method for identifying the binding sites of cellular RNA-binding proteins. RIP-Chip: Similar to ChIP-Seq, but does ... bound to a protein of interest. MNase mediated cleavage produces a library of target DNA sites bound to a protein of interest ... ChiRP-Seq: Measures RNA-bound DNA and proteins. ChIP-exo: Employs exonuclease treatment to achieve up to single base-pair ... These transcription factor-MNase fusion proteins can cleave DNA around the DNA-binding site of the protein of interest. In the ...
RBPmap: mapping binding sites of RNA binding proteins. Retrieved on 2020-8-02. Pfefferle S, Schöpf J, Kögl M, Friedel CC, ... The mRNA of C20orf27 has about 23 predicted mRNA binding protein binding sites which sequences are also conserved in evolution ... variant 2 and variant 3 encodes the same protein isoform and this second protein isoform is shorted than the protein isoform ... Transcription binding matrix, like EGR/nerve growth factor induced protein C & related factors, GC-Box factors SP1/GC, Krueppel ...
This domain can bind proteins and RNA independently, even if the other binding domains are not present. Although this domain is ... The RRMs play a role in RNA binding, while the AcD engages in protein-protein interactions (PPIs). The RGG box is involved in ... Kiledjian M, Dreyfuss G (1992). "Primary structure and binding activity of the hnRNP U protein: Binding RNA through RGG box". ... The hnRNPs are RNA-binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). SYNCRIP is made up of an N- ...
Ro protein binds to Y RNA. Epidemiology[edit]. Approximately only 0.1 to 0.5 percent of the general population has the antibody ...
Ito D, Suzuki N (October 2011). "Conjoint pathologic cascades mediated by ALS/FTLD-U linked RNA-binding proteins TDP-43 and FUS ... Wolozin B, Apicco D (2015). "RNA binding proteins and the genesis of neurodegenerative diseases". Advances in Experimental ... and TAR DNA-binding protein-43 (TDP-43). In all of these instances, an aberrant form of the protein itself appears to be the ... increases the tendency of a specific protein to bind to itself. In this aggregated form, the protein is resistant to clearance ...
This protein bears similarity to nuclear RNA-binding proteins; however, it has not been demonstrated that this protein binds ... "The human RD protein is closely related to nuclear RNA-binding proteins and has been highly conserved". Gene. 90 (2): 299-302. ... "Entrez Gene: RDBP RD RNA binding protein". Narita T, Yamaguchi Y, Yano K, Sugimoto S, Chanarat S, Wada T, Kim DK, Hasegawa J, ... The protein encoded by this gene is part of a complex termed negative elongation factor (NELF) which represses RNA polymerase ...
"RNA Binding Protein/RNA Element Interactions and the Control of Translation". Current Protein & Peptide Science. 13 (4): 294- ... and membrane proteins. The poly(A) tail contains binding sites for poly(A) binding proteins (PABPs). These proteins cooperate ... The most common structure is a stem-loop, which provides a scaffold for RNA binding proteins and non-coding RNAs that influence ... CPE-binding protein (CPEB) binds to CPEs in conjunction with a variety of other proteins in order to elicit different responses ...
Jung Y, El‐Manzalawy Y, Dobbs D, Honavar VG (2019). Partner‐specific prediction of RNAbinding residues in proteins: A critical ... analysis and prediction of protein-protein, protein-RNA, and protein-DNA interfaces and interactions, social network analytics ... Walia, R., El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2017). Sequence-based Prediction of RNA-binding Residues in Proteins. ... Towfic, F.; Caragea, C.; Dobbs, D.; Honavar, V. (2010). "Struct-NB: Predicting protein-RNA binding sites using structural ...
RBPmap, which maps predicted binding sites of RNA binding proteins, showed multiple conserved motifs in evolution relative to ... "RBPmap - Motifs Analysis and Prediction of RNA Binding Proteins". Archived from the original on 22 ... Based on Protein Abundance Database (PAXdb 4.1), the human protein of ISLR is shown with high protein abundance (ppm value > 1 ... Current RNA-seq studies show that the protein is highly expressed in the endometrium and ovary and shows expression among 25 ...
MSI2: encoding protein Musashi RNA binding protein 2. *MYBBP1A: encoding protein Myb-binding protein 1A ... encoding protein Long intergenic non-protein coding RNA 511. *LINC00674 encoding protein Long intergenic non-protein coding RNA ... VPS25: encoding protein Vacuolar protein-sorting-associated protein 25. *VPS53: encoding protein Vacuolar protein sorting 53 ... encoding protein Phosphoribosyl pyrophosphate synthetase-associated protein 2. *QRICH2: encoding protein Glutamine-rich protein ...
Work with zebrafish and mammals suggest a further interplay between miRNA and RNA-binding proteins (RBPs) in determining ... Kedde M, Agami R (April 2008). "Interplay between microRNAs and RNA-binding proteins determines developmental processes". Cell ... Research on Caenorhabditis elegans suggests that multiple mechanisms including RNA regulation may play a role in maintaining ...
Hofmann JW, Seeley WW, Huang EJ, Kubota M (24 January 2019). "RNA Binding Proteins and the Pathogenesis of Frontotemporal Lobar ... They consist of tau fibrils as a major component together with a number of other protein products including ubiquitin and ... is caused by mutations in the MAPT gene on chromosome 17 that encodes the tau protein. It has been determined that there is a ...
RBM proteins constitute a large family of RNA-binding proteins (RBPs). There are 52 RBM proteins (HGNC: HUGO Gene Nomenclature ... RNA-binding motif 10 is a protein that is encoded by the RBM10 gene. This gene maps on the X chromosome at Xp11.23 in humans. ... Yin LL, Wen XM, Li M, Xu YM, Zhao XF, Li J, Wang XW (November 2018). "A gene mutation in RNA-binding protein 10 is associated ... May 2019). "RNA-binding protein RBM6 as a tumor suppressor gene represses the growth and progression in laryngocarcinoma". Gene ...
... of RNA-Binding proteins revealed the oncogenic property of six RBPs (NSUN6, ZC3H13, BYSL, ELAC1, RBMS3, and ... Pan-Cancer analysis of RNA-Binding Proteins across Human Cancers also were constructed to explore the expression, somatic copy ... Pan-Cancer Analysis And Networks Of lncRNAs, microRNAs, CeRNAs And RNA-Binding Proteins(RBPs) Nature's Landing Page for the ... Recently, Pan-Cancer resources were created for the Networks Of lncRNAs, microRNAs, CeRNAs and RNA-Binding Proteins (RBPs). The ...
Hentze's research focuses on RNA biology and RNA-binding proteins. In 1987, Hentze and his colleagues discovered iron- ... Hentze, MW; Castello, A; Schwarzl, T; Preiss, T (2018-01-17). "A brave new world of RNA-binding proteins" (PDF). Nat Rev Mol ... Recently, Hentze and his colleagues discovered new RNA-binding motives of proteins which they unraveled using a newly developed ... Hentze's research group has paved the way for understanding translational control (RNA-binding proteins, microRNAs) whose ...
DUF4463 is cytosolic and distantly homologous to RNA-binding proteins. This domain can be used to determine the orientation of ... Transmembrane protein 63A is a protein that in humans is encoded by the TMEM63A gene. The mature human protein is approximately ... The 3' UTR is predicted to be bound by the regulatory element miR-9/9ab. The mature form of the human TMEM63A protein has 807 ... The protein has three isoforms. The mature protein is designated isoform CRA. The other two isoforms are X1 and X2, which are ...
Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System. PLoS ... RNA-binding proteins in human genetic disease. Trends in genetics: TIG. 2008-08-01, 24 (8): 416-425. ISSN 0168-9525. PMID ... PRIDB: a protein-RNA interface database. Nucleic Acids Research. 2016-11-07, 39 (Database issue): D277-D282. ISSN 0305-1048. ... 病毒基因组(DNA或RNA)非常紧密地包装在病毒衣壳中[4][5]。因此,许多病毒只不过是有组织的核
Zinc finger RNA binding protein is a protein in humans that is encoded by the ZFR gene. "Entrez Gene: Zinc finger RNA binding ...
The 5' UTR is bound by the RNA binding proteins RBMX1, FUS, SFRS1, ACO1, and NONO. The 3' UTR is bound by EIF4B, A2BP1, and ... "The Database of RNA-binding protein specificities". RBPDB. University of Toronto. Retrieved 1 May 2018. Stothard, Paul. " ... Protein FAM208B (family with sequence similarity 208 member b) is a protein that in humans is encoded by the FAM208B gene. The ... The promoter contains binding sites for Ikaros2, Nuclear Factor Y, and at least three binding sites for Pleomorphic adenoma ...
This gene encodes an RNA-binding protein that is a member of the Musashi protein family. The encoded protein is transcriptional ... Musashi-2, also known as Musashi RNA binding protein 2, is a protein that in humans is encoded by the MSI2 gene. Like its ... "Entrez Gene: Musashi RNA binding protein 2". de Andrés-Aguayo L, Varas F, Graf T (July 2012). "Musashi 2 in hematopoiesis". ... As an RNA-binding protein, MSI2 is acts as a translational inhibitor. Through this molecular mechanism, MSI2 contributes in ...
1999). "The c-myc coding region determinant-binding protein: a member of a family of KH domain RNA-binding proteins". Nucleic ... 2000). "H19 RNA binds four molecules of insulin-like growth factor II mRNA-binding protein". J. Biol. Chem. 275 (38): 29562-9. ... Yisraeli JK (2005). "VICKZ proteins: a multi-talented family of regulatory RNA-binding proteins". Biol. Cell. 97 (1): 87-96. ... The protein encoded by this gene contains four K homology domains and two RNA recognition motifs. It functions by binding to ...
Senataxin interacts with RNA polymerase II and poly(A) binding proteins. At the C-terminal, senataxin has a DEAD box helicase ... The senataxin protein, which has RNA-DNA helicase activity, and DHX9 human helicase can resolve R-loops. This allows XRN2, an ... Meanwhile, the C-terminus encodes the DNA/RNA helicase activity. Similarly, SETX encodes the senataxin protein that has a N- ... This gene encodes a protein named senataxin, a 302kDa protein There is high homology between human SETX and yeast Sen1. Sen1 in ...
"RNA polymerase II-associated protein (RAP) 74 binds transcription factor (TF) IIB and blocks TFIIB-RAP30 binding". J. Biol. ... Sopta M, Carthew RW, Greenblatt J (1985). "Isolation of three proteins that bind to mammalian RNA polymerase II". J. Biol. Chem ... a transcriptional activator that interacts with multiple domains of cAMP-responsive element-binding protein (CREB)-binding ... Kim JB, Yamaguchi Y, Wada T, Handa H, Sharp PA (Sep 1999). "Tat-SF1 protein associates with RAP30 and human SPT5 proteins". Mol ...
The encoded protein contains several KH domains, which are important in RNA binding and are known to be involved in RNA ... Yisraeli JK (2005). "VICKZ proteins: a multi-talented family of regulatory RNA-binding proteins". Biol. Cell. 97 (1): 87-96. ... Insulin-like growth factor 2 mRNA-binding protein 3 is a protein that in humans is encoded by the IGF2BP3 gene. The protein ... 2006). "Analysis of RNA-binding protein IMP3 to predict metastasis and prognosis of renal-cell carcinoma: a retrospective study ...
RNA polymerase II regulatory region sequence-specific DNA binding. • DNA binding. • sequence-specific DNA binding. • ... Homeobox protein Hox-D8 is a protein that in humans is encoded by the HOXD8 gene.[5][6][7] ... transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding. • RNA ... negative regulation of transcription from RNA polymerase II promoter. • positive regulation of transcription from RNA ...
positive regulation of transcription from RNA polymerase II promoter. • حمل أنثوي. • positive regulation of cell proliferation ... J Protein Chem. 7 (4): 325-39. PMID 3151250. doi:10.1007/BF01024882. تحقق من التاريخ في: ,date=. (مساعدة) ... "Cysteine residues in a synthetic peptide corresponding to human follicle-stimulating hormone beta-subunit receptor-binding ...
The specific diagnosis of EVD is confirmed by isolating the virus, detecting its RNA or proteins, or detecting antibodies ... ability to bind to and infect targeted cells.[51] The viral RNA polymerase, encoded by the L gene, partially uncoats the ... which code for proteins with antiviral properties.[51] EBOV's V24 protein blocks the production of these antiviral proteins by ... Once interferon has bound to its receptors on the neighbouring cell, the signalling proteins STAT1 and STAT2 are activated and ...
This membrane protein-related article is a stub. You can help Wikipedia by expanding it.. *v ... Chloride conductance of these channels can be modulated by agents such as benzodiazepines that bind to the GABA-A receptor. At ... Gamma-aminobutyric acid receptor subunit alpha-4 is a protein that in humans is encoded by the GABRA4 gene.[5][6] ... GABRA4+protein,+human at the US National Library of Medicine Medical Subject Headings (MeSH) ...
Protein synthesisEdit. See also: Transcription and translation. Protein synthesis within chloroplasts relies on an RNA ... Five subunits of the TOC complex have been identified-two GTP-binding proteins Toc34 and Toc159, the protein import tunnel ... Hundreds of different PPR proteins from the nuclear genome are involved in the RNA editing process. These proteins consist of ... 14-3-3 proteins only bind to chloroplast preproteins.[43] It is also bound by the heat shock protein Hsp70 that keeps the ...
protein kinase inhibitor activity. • collagen binding. • extracellular matrix structural constituent conferring compression ... negative regulation of protein kinase activity. • cytokine-mediated signaling pathway. • negative regulation of JAK-STAT ... a newly discovered member of the leucine-rich repeat protein family". The Journal of Biological Chemistry. 276 (15): 12212-21. ... a novel member of the leucine-rich repeat protein family closely related to decorin and biglycan". The Journal of Biological ...
protein binding. • transcription regulatory region DNA binding. • RNA polymerase II core promoter sequence-specific DNA binding ... transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding. • RNA polymerase ... RNA polymerase II transcription factor activity, sequence-specific DNA binding. • transcriptional activator activity, RNA ... DNA binding. • sequence-specific DNA binding. • transcription factor activity, sequence-specific DNA binding. • ...
... a PDZ-domain and LIM-domain protein, binds to alpha-actinin-1 and associates with actin filaments and stress fibers in ... cadherin binding involved in cell-cell adhesion. • actin binding. • muscle alpha-actinin binding. ... "Towards a proteome-scale map of the human protein-protein interaction network.". Nature. 437 (7062): 1173-8. PMID 16189514. doi ... Vallenius T، Mäkelä TP (2003). "Clik1: a novel kinase targeted to actin stress fibers by the CLP-36 PDZ-LIM protein.". J. Cell ...
steroid binding. • protein binding. • enzyme binding. • receptor binding. • lipid binding. • RNA polymerase II transcription ... identical protein binding. • RNA polymerase II transcription factor activity, sequence-specific DNA binding. • transcriptional ... DNA binding. • sequence-specific DNA binding. • transcription factor activity, sequence-specific DNA binding. • ATPase binding ... RNA polymerase II core promoter proximal region sequence-specific binding. • metal ion binding. • RNA polymerase II core ...
GTP binding. • ربط بروتيني. • structural molecule activity. • GTPase activity. • protein complex scaffold activity. • binding, ... v2 is a parkin-binding protein". Brain Research. Molecular Brain Research. 117 (2): 179-89. PMID 14559152. doi:10.1016/S0169- ... protein ligase and promotes the degradation of the synaptic vesicle-associated protein, CDCrel-1". Proceedings of the National ... Beites CL، Xie H، Bowser R، Trimble WS (May 1999). "The septin CDCrel-1 binds syntaxin and inhibits exocytosis". Nature ...
IgLON perekond koosneb neljast liikmest: LSAMP (limbic system-associated membrane protein), Neurotrimin(Ntm)/CEPU-1 (vastavalt ... mis lõigatakse primaarsest RNA transkriptist välja) asuvad Ig3 poolt kodeerivate alade vahel. Ig2 asub eksonites 3 ja 4 ning ... roti ja kana ortoloogid), OBCAM (opioid-binding cell adhesion molecule) ja Kilon/Neurotractin (vastavalt roti ja kana ... 10,0 10,1 10,2 Reed, J., McNamee, C., Rackstraw, S., Jenkins, J., Moss, D. (2004). Diglons are heterodimeric proteins composed ...
Receptor binding, as well as membrane fusion, are catalyzed by the protein E, which changes its conformation at low pH, causing ... "An RNA Pseudoknot Is Required for Production of Yellow Fever Virus Subgenomic RNA by the Host Nuclease XRN1". Journal of ... and forms a complex with protein E. The immature particles are processed in the Golgi apparatus by the host protein furin, ... Yellow fever is caused by yellow fever virus, a 40- to 50-nm-wide enveloped RNA virus, the type species and namesake of the ...
Small acid-soluble proteins (SASPs) are found in endospores. These proteins tightly bind and condense the DNA, and are in part ... and the sigma factor subunits of RNA polymerase. ... Small acid-soluble proteins (SASPs) saturate the endospore's ... The dipicolinic acid helps stabilize the proteins and DNA in the endospore.[14]:141 Next the peptidoglycan cortex forms between ... In Bacillus subtilus endospores, the spore coat is estimated to contain more than 70 coat proteins, which are organized into an ...
Non-coding RNA or "RNA genes". These are a broad class of genes that encode RNA which is not translated into protein. The most ... It needs a range of transcription factors to bind it to promoters. ... RNA polymerase IV synthesizes siRNA in plants.[5]. *RNA polymerase V synthesizes RNAs involved in siRNA-directed ... Transfer RNA (tRNA)-transfers specific amino acids to growing polypeptide chains at the ribosomal site of protein synthesis ...
PDZ domain binding. • cadherin binding. • peptidase activity. • beta-catenin binding. • protein binding. • calcium channel ... negative regulation of transcription from RNA polymerase II promoter. • proteolysis. • regulation of synaptic plasticity. • ... positive regulation of protein binding. • positive regulation of protein import into nucleus, translocation. • Notch receptor ... protein processing. • protein maturation. • myeloid dendritic cell differentiation. • autophagy. • protein glycosylation. • ...
The active site is a region on an enzyme which a particular protein or substrate can bind to. The active site will only allow ... and when methotrexate binds the enzyme, it renders it inactive, so it cannot synthesize DNA and RNA.[3] Thus, the cancer cells ... is modified to include binding of the inhibitor to the free enzyme:. EI. +. S. ⇌. k. 3. k. −. 3. E. +. S. +. I. ⇌. k. −. 1. k. ... When a competitive inhibitor is bound to an enzyme the K. m. {\displaystyle K_{m}}. increases. This means the binding affinity ...
chromatin binding. • DNA polymerase binding. • protein C-terminus binding. • protein binding. • four-way junction DNA binding. ... messenger RNA. [13]. Breast cancer (progesteron receptor negative). Over-expression. -. messenger RNA. [16]. ... identical protein binding. • endodeoxyribonuclease activity. • ATP binding. • single-stranded DNA binding. • double-stranded ... This protein can interact with the ssDNA-binding protein RPA, BRCA2, PALB2[10] and RAD52. ...
Precursor proteins also have an effect on VPg-CRE specificity and stability. The upper RNA stem loop, to which VPg binds, has a ... The genome RNA is unusual because it has a protein on the 5' end that is used as a primer for transcription by RNA polymerase. ... strand RNA genome is replicated through a double-stranded RNA intermediate that is formed using viral RDRP (RNA-Dependent RNA ... B3 RNA-dependent RNA polymerase in complex with its protein primer VPg confirms the existence of a second VPg binding site on ...
... with similar protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene's ... No membrane-bound organelles (questioned[56]) or nucleus. No membrane-bound organelles or nucleus. Membrane-bound organelles ... although there are many introns in their transfer RNA and ribosomal RNA genes,[146] and introns may occur in a few protein- ... Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular RNA ...
PMFBP1: encoding protein Polyamine-modulated factor 1-binding protein 1. *POLR3K: encoding enzyme DNA-directed RNA polymerase ... LINC00273 encoding protein Long intergenic non-protein coding RNA 273. *LOC124220: encoding protein Zymogen granule protein 16 ... SHCBP1: encoding protein SHC SH2 domain-binding protein 1. *SLZ1: encoding protein SLX1 structure-specific endonuclease subunit ... UNKL: encoding protein RING finger protein unkempt-like. *VAT1L: encoding protein Vesicle amine transport protein 1 homolog (T ...
TATA-binding protein (TBP) can be recruited in two ways, by SAGA, a cofactor for RNA polymerase II, or by TFIID.[11] When ... binds to the TATA box at its TATA-binding protein (TBP) subunit.[3] TBP binds to the minor groove[15] of the TATA box via a ... Transcription factors, TATA binding protein (TBP), and RNA polymerase II are all recruited to begin transcription. ... The TATA box is the binding site of the TATA-binding protein (TBP) and other transcription factors in some eukaryotic genes. ...
... and is likely bound by other proteins to exert a repressive function. Another polycomb complex, PRC1, can bind H3K27me3[69] and ... This protein associates with elongating RNA polymerase II, and H3K36Me3 is indicative of actively transcribed genes.[64] ... Gamma H2AX acts as a binding site for the protein MDC1, which in turn recruits key DNA repair proteins[86] (this complex topic ... "A novel zinc finger protein is associated with U7 snRNP and interacts with the stem-loop binding protein in the histone pre- ...
Important information on protein synthesis, ligand binding and RNA interaction can be obtained using this novel technique at ... This bacterial protein complex is a machine for folding other proteins, which get trapped within the shell. Fatty acid synthase ... Proteins in vitreous ice usually adopt a random distribution of orientations (or viewing angles), allowing a fairly isotropic ... These often enable the user to manually dock in protein coordinates (structures from X-ray crystallography or NMR) of subunits ...
NMR is also useful for probing the binding of nucleic acid molecules to other molecules, such as proteins or drugs. This can be ... such as DNA or RNA. It is useful for molecules of up to 100 nucleotides, and as of 2003, nearly half of all known RNA ... or by cross-saturation experiments where one of the binding molecules is selectively saturated and, if bound, the saturation ... Interactions between RNA and metal ions can be probed by a number of methods, including observing changes in chemical shift ...
... the adenovirus E1A proteins bind to the retinoblastoma gene product". Nature. 334 (6178): 124-9. Bibcode:1988Natur.334..124W. ... RNA interference (RNAi) and small-RNA biology; DNA replication; RNA splicing; signal transduction; genome structure; non-coding ... a highly conserved protein complex that recognizes and binds to specific DNA sequences, marking starting points for replication ... A.D. Hershey and Martha Chase, "Independent Functions of Viral Protein and Nucleic Acid in Growth of Bacteriophage," J. General ...
Nguyen VT, Kiss T, Michels AA, Bensaude O (2001). "7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T ... Cyclin-T2 is a protein that in humans is encoded by the CCNT2 gene. The protein encoded by this gene belongs to the highly ... "Analysis of the effect of natural sequence variation in Tat and in cyclin T on the formation and RNA binding properties of Tat- ... "The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent ...
In 1993, Alan Hall was awarded the Feldberg Foundation Prize for his work on the role GTP-binding proteins played on signal ... evidence of the importance of Ral was provided when cortical neurons were depleted of endogenous RalA and RalB isoforms by RNA ... Finally, Ral mutants unable to bind to their specific effector proteins showed that RalA and RalB isoforms promote branching ... "The small GTP-binding protein rac regulates growth factor-induced membrane ruffling". Cell. 70 (3): 401-410. doi:10.1016/0092- ...
The encoded protein can also bind RNA and decreases the stability of some mRNAs. The genes of the alpha and beta subunits of ... GO:0001948 protein binding. • catalytic activity. • transferase activity, transferring acyl groups. • 3-hydroxyacyl-CoA ... RNA binding. • acetyl-CoA C-acyltransferase activity. • long-chain-enoyl-CoA hydratase activity. ... HADHB has been shown to bind to the distal 3' untranslated region of renin mRNA, thereby regulating renin protein expression.[ ...
Wnt-protein binding. • protein binding. • protein kinase binding. • ubiquitin protein ligase binding. • transmembrane signaling ... positive regulation of transcription from RNA polymerase II promoter. • negative regulation of cell proliferation. • signal ... gene family encode 7-transmembrane domain proteins that are receptors for Wnt signaling proteins. The FZD5 protein is believed ... Katoh Y, Katoh M (2007). "Conserved POU-binding site linked to SP1-binding site within FZD5 promoter: Transcriptional ...
RNA virus. CBV. HAV (A). HCV (C). HDV (D). HEV (E). HGV (G). ... the three capsid protein genes (green and blue), the agnogene ( ... "Transcription factor Spi-B binds unique sequences present in the tandem repeat promoter/enhancer of JC virus and supports ... RNA virus. HCV Hepatocellular carcinoma. Splenic marginal zone lymphoma. HTLV-I Adult T-cell leukemia/lymphoma. ... RNA virus. MeV Subacute sclerosing panencephalitis. LCV Lymphocytic choriomeningitis. Arbovirus encephalitis. Orthomyxoviridae ...
Z. J. Lorković and A. Barta, "Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from ... N. V. Fedoroff, "RNA-binding proteins in plants: the tip of an iceberg?" Current Opinion in Plant Biology, vol. 5, no. 5, pp. ... RNA-Binding Proteins in Plant Immunity. Virginia Woloshen,1,2 Shuai Huang,1,2 and Xin Li1,2 ... Z. Q. Fu, M. Guo, B. R. Jeong et al., "A type III effector ADP-ribosylates RNA-binding proteins and quells plant immunity," ...
... stability and translation of coding and non-coding RNAs. RNA-binding proteins (RBPs) and ribonucleoproteins coordinate RNA ... A census of human RNA-binding proteins.. Gerstberger S1, Hafner M2, Tuschl T1. ... Our analysis is a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism. ... Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, New York ...
Addition of several general RNA binding proteins, such as hnRNP A1, La autoantigen, pyrimidine tract binding protein (hnRNP I/ ... General RNA binding proteins render translation cap dependent.. Svitkin YV1, Ovchinnikov LP, Dreyfuss G, Sonenberg N. ... we suggest that one function of general mRNA binding proteins in the cytoplasm is to promote ribosome binding by a 5 end, cap- ... we show that a critical parameter which contributes to cap-dependent translation is the amount of general RNA binding proteins ...
... the RNA-binding protein training dataset of 2752 proteins and the RNA-binding protein testing dataset of 1374 proteins (see ... iv) The RNA-Binding Protein Dataset:. protein sequences with length ,6000 aa or ,50 aa were removed since they might be protein ... means RNA-binding protein and "B" means RNA-nonbinding protein) are available in Supplementary Material (see Supplementary ... Prediction of RNA-Binding Proteins by Voting Systems. C. R. Peng,1,2 L. Liu,1 B. Niu,3 Y. L. Lv,4 M. J. Li,2 Y. L. Yuan,5 Y. B ...
We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their ... InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites ... GO:0003676 nucleic acid binding GO:0003723 RNA binding GO:0003729 mRNA binding ...
The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins. RNA 3:1421-1433. ... This review focuses on RNA-binding proteins and their role in regulating local protein synthesis in neurons. ... Such a mechanism was recently attributed to the mRNA-binding protein zipcode binding protein 1 (ZBP1) (Huttelmaier et al., 2005 ... RNA-Binding Proteins: A Lesson in Repression. David G. Wells. Journal of Neuroscience 5 July 2006, 26 (27) 7135-7138; DOI: ...
... 18.10.2016. Small regulatory RNA molecules are vital for salmonella and other ... This protein and the RNA molecules that bind to it represent a largely unresearched class of gene activity regulators in the ... The structures of the different regulatory RNA molecules are shown left, their preferred protein binding partners on the right ... Experiments showed that the ProQ protein binds to 98 regulatory RNAs of the enterobacterial Salmonella enterica. The bacterium ...
In this review we focus on the effect of alcohol on different RNA-binding proteins and their possible contribution to alcohol- ... Given their diverse functions, cells express a variety of RNA-binding proteins, which play important roles in the pathologies ... We further discuss the conventional methods and newer techniques that are employed to identify RNA-binding proteins. ... related disorders, and discuss the role of these proteins in the development of neurological diseases and cancer. ...
RNA-binding proteins (RBPs) regulate all aspects of RNA metabolism, such as splicing, localization, translation, and ... Regulation by RNA-binding proteins : sequence determinants and evolutionary dynamics. Author(s). Alexis, Maria Sarah. ... RBPs regulate RNA processing by recognizing RNA sequence elements (motifs) within RNAs. Studying the determinants of these RBP: ... Second, I present a comprehensive study of the affinity landscapes of 78 human RBPs using RNA Bind-N-Seq (RBNS), an unbiased ...
Twentyeight-Seven is building a small molecule platform to target interactions between non-coding RNAs and an emerging target ... Twentyeight-Sevens bet on RNA-binding proteins. Twentyeight-Seven is capitalizing on the emerging biology of RNA-binding ... RNA-binding proteins.. Launched last September, the company is using an $82.8 million series A round backed by a syndicate that ... class in gene regulation: RNA-binding proteins. ... proteins by targeting their interactions with non-coding RNAs. ...
... associated with characterized mutant phenotypes in C. elegans.. RBP gene. RNA binding domain. ... RNA binding specificity of most RBPs is unknown because their RNA targets are not identified yet. However, RNA binding ... RNA-binding proteins (RBPs) play key roles in post-transcriptional control of RNAs, which, along with transcriptional ... RNA-binding proteins* Min-Ho Lee § †, Tim Schedl§ Department of Genetics, Washington University School of Medicine, St. Louis, ...
Approximately 6%-8% of all proteins are RNA-binding proteins (RBPs). Distinguishing these RBPs or their binding residues is a ... and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and ... Alternatively, researchers have developed many computational approaches to predict RBPs and protein-RNA binding sites, by ... Previously, a number of experimental methods were developed for the determination of protein-RNA interactions. However, these ...
Human cells encode thousands of RNA-binding proteins with u … ... allow cells to carry out pre-RNA processing and post- ... Our results show specific enrichment of many known RNA-binding regions on many known RNA-binding proteins, confirming the ... Keywords: RNA-binding proteins; RNA-binding regions; mass spectrometry; single-shot MS analysis. ... Human cells encode thousands of RNA-binding proteins with unique RNA-binding properties. These properties are regulated through ...
Bovine Viral Diarrhea Virus Core Is an Intrinsically Disordered Protein That Binds RNA Catherine L. Murray, Joseph ... Insulin-Like Growth Factor II mRNA Binding Protein 1 Associates with Gag Protein of Human Immunodeficiency Virus Type 1, and ... Protease Activity, Self Interaction, and Small Interfering RNA Binding of the Silencing Suppressor P1b from Cucumber Vein ... Virp1 Is a Host Protein with a Major Role in Potato Spindle Tuber Viroid Infection in Nicotiana Plants K. Kalantidis, M. A. ...
But production of the protein is reactivated in many types of aggressive cancer, and it is associated with poor prognosis in ... New findings from UC Santa Cruz point toward a possible mechanism by which this protein drives metastasis. ... The RNA binding protein IGF2BP3 is normally active in fetal tissue and undetectable in most adult tissue. ... Malignancy-associated gene network regulated by an RNA binding protein Study of protein-RNA interactions in pancreatic cancer ...
rna-binding proteins. 15 January 2021. Welcome: Olivier Duss 27 April 2020. Helping researchers identify host proteins used by ...
Several in vitro studies have demonstrated that the Hu proteins bind to RNA. HuB was found to bind to AU-rich RNA sequences in ... complexity of the Hu RNA binding proteins. Our work illustrates several levels of complexity in the family of Hu RNA binding ... 1993b) The protein product of the fragile X gene, FMR-1, has characteristics of an RNA-binding protein. Cell 74:291-298. ... 1993) The Drosophila gene rbp9 encodes a protein that is a member of a conserved group of putative RNA binding proteins that ...
"RNA-Binding Proteins" by people in Harvard Catalyst Profiles by year, and whether "RNA-Binding Proteins" was a major or minor ... Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind ... "RNA-Binding Proteins" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical ... Double-Stranded RNA-Binding Proteins*Double-Stranded RNA-Binding Proteins. *Double Stranded RNA Binding Proteins ...
Circular RNAs (circRNAs) are increasingly recognized as having a role in cancer development. Their expression is modified in ... Identification of Novel RNA Binding Proteins Influencing Circular RNA Expression in Hepatocellular Carcinoma Int J Mol Sci. ... Keywords: ESRP2; RNA binding proteins (RBPs); circular RNA (circRNA); hepatocellular carcinoma (HCC). ... Using publicly available datasets, we identified RNA binding proteins (RBPs) with enriched motifs around the splice sites of ...
The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Zhicheng Dong, Meng-Hsuan Han, ... 2004) Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10:185-191. ... The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1 ... The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1 ...
... the QKI-6 and QKI-7 RNA binding proteins are positive regulators of PNS myelination and show that the QKI RNA binding proteins ... or RNA binding proteins in PNS myelination. Methodology/Principal Findings To define the role of the QKI proteins in PNS ... In addition, these events were coordinated with elevated proteins levels of p27KIP1 and myelin basic protein (MBP), markers of ... little is known about the role of the QKI proteins, ...
1999) Degradation of FinP antisense RNA from F-like plasmids: The RNA-binding protein, FinO, protects FinP from ribonuclease E ... A more functionally relevant criterion is the association of RNAs with cognate RNA-binding proteins. Here, we describe the ... One such criterion is the association of RNAs with functionally important cognate RNA-binding proteins. Here we analyze the ... Grad-seq promises to define functional RNA classes and major RNA-binding proteins in both model species and genetically ...
Binds directly to the 3-UTR of the PER1 mRNA (By similarity). ... RNA-binding protein 4B. Alternative name(s):. RNA-binding motif ... sp,Q9BQ04,RBM4B_HUMAN RNA-binding protein 4B OS=Homo sapiens GN=RBM4B PE=1 SV=1 ... Protein. Similar proteins. Organisms. Length. Cluster ID. Cluster name. Size. Q9BQ04. G7NC45. G3R7Q9. G7PP84. H2NCQ1. H2Q476. ... RNA binding Source: UniProtKB ,p>Inferred from Direct Assay,/p> ,p>Used to indicate a direct assay for the function, process or ...
May bind to specific miRNA hairpins (By similarity). ... Binds to RNA homopolymers, with a preference for poly(G) and ... RNA-binding motif protein 10. RNA-binding protein S1-11 Publication. ,p>Manually curated information that is based on ... RNA-binding protein 10Add BLAST. 852. Amino acid modifications. Feature key. Position(s). DescriptionActions. Graphical view. ... "Molecular cloning of a RNA binding protein, S1-1.". Inoue A., Takahashi K., Kimura M., Watanabe T., Morisawa S.. Nucleic Acids ...
... it makes a speckled pattern consistent with the large protein/RNA complexes formed by RNA-binding proteins. Bowser suspects it ... RNA-binding Protein Inhabits Granules in ALS, FTD. Go to another part. Series - 10th Brain Research Conference: RNA Metabolism ... Li thinks RBM45 must bind RNAs as an oligomer. The researchers are now trying to identify the RNAs that bind both RBM43 and TDP ... Role of Stress Granules and RNA-Binding Proteins in Neurodegeneration: A Mini-Review. Gerontology. 2013;59(6):524-33. PubMed. ...
... led by Dr Enrique Lara Pezzi at the Centro Nacional de Investigaciones Cardiovasculares has identified the RNA-binding protein ... RNA-binding proteins perform important tasks in the cell.. In this study, we have investigated the role of the RBP SRSF3 in the ... RNA-binding protein SRSF3 appears to be key factor for proper heart contraction, survival. *Download PDF Copy ... has identified the RNA-binding protein SRSF3 as an essential factor for proper heart contraction and survival. In a study ...
Gene Regulation at the RNA Layer: RNA Binding Proteins in Intercellular Signaling Networks ... Gene Regulation at the RNA Layer: RNA Binding Proteins in Intercellular Signaling Networks ... Gene Regulation at the RNA Layer: RNA Binding Proteins in Intercellular Signaling Networks ... Gene Regulation at the RNA Layer: RNA Binding Proteins in Intercellular Signaling Networks ...
RNA binding proteins (RBP) regulate the expression level and isoform of proteins within the cell in an often spatially and ... our understanding of sequence specific binding of RNA and aid the development of protein-based approaches to target RNAs ... Protein-RNA interactions play a central role in post-transcriptional regulation. By interacting with precursor and mature mRNA ... I also apply my technique to suggest changes to a RNA recognition motif aimed at re-targeting the domain to specifically bind a ...
... that some forms of amyotrophic lateral sclerosis and frontotemporal dementia are due to defects in a single RNA-binding protein ... Maintaining the balance of RNA-binding proteins.. (A) RNA-binding proteins (red, green, orange, purple, and blue), such as TDP- ... be transcribed into RNA molecules that soak up RNA-binding proteins and prevent these proteins from carrying out their ... B) A mutation in a gene called C9orf72 can result in a reduction in the solubility of an RNA-binding protein known as hnRNP H ( ...
  • RNA-binding proteins (RBPs) and ribonucleoproteins coordinate RNA processing and PTGR. (
  • Here, we present a census of 1,542 manually curated RBPs that we have analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression. (
  • In this review we provide a succinct overview of the role of RNA-binding proteins (RBPs) in regulating gene expression. (
  • We have divided the review into subheadings under which we discuss the effect of alcohol on RNA-binding proteins, RNA-binding proteins in neurological diseases and cancer, and finally the methods employed to identify RBPs and/or ligands of a RBP. (
  • As mRNA molecules emerge from the nucleus, bound nuclear proteins are often replaced with a new set of RNA-binding proteins (RBPs). (
  • In fact RBPs are involved in every step of the RNA lifecycle, e.g., transport of mRNA to the site of translation, storage and mRNA degradation ( Figure 1 ) [ 1 ]. (
  • RBPs regulate RNA processing by recognizing RNA sequence elements (motifs) within RNAs. (
  • Studying the determinants of these RBP:RNA interactions is therefore key to understanding how RBPs select their targets, and how RNA processing evolves over time. (
  • Second, I present a comprehensive study of the affinity landscapes of 78 human RBPs using RNA Bind-N-Seq (RBNS), an unbiased assay that determines the sequence, structure, and context preferences of RBPs. (
  • Offsetting this trend, RBPs show extensive preferences for contextual features distinct from short linear motifs, including spaced "bipartite" motifs, biased flanking nucleotide composition, and bias away from or toward RNA structure. (
  • These results emphasize the importance of contextual features in RNA recognition, which likely enable targeting of distinct subsets of transcripts by different RBPs that recognize the same linear motif. (
  • genome encodes many RNA-binding proteins (RBPs) with diverse functions in development, indicative of extensive layers of post-transcriptional control of RNA metabolism. (
  • In addition, several RBPs that bind regulatory sequences in the 3'untranslated regions of mRNAs have been identified molecularly. (
  • It is likely that most RBPs regulate multiple RNA targets. (
  • Such studies will provide insights into how RBPs exert coordinate control of their RNA targets, thereby affecting development in a concerted fashion. (
  • RNA-binding proteins (RBPs) play key roles in post-transcriptional control of RNAs, which, along with transcriptional regulation, is a major way to regulate patterns of gene expression during development. (
  • Many RBPs have one or more copies of the same RNA binding domain while others have two or more distinct domains. (
  • Even though the mechanisms by which RBPs influence protein expression patterns in their respective tissues are still poorly understood, the association of many RBPs with mutant phenotypes underscores their importance in C. elegans development ( Table 1 ). (
  • Approximately 6%-8% of all proteins are RNA-binding proteins (RBPs). (
  • Distinguishing these RBPs or their binding residues is a major aim of structural biology. (
  • Alternatively, researchers have developed many computational approaches to predict RBPs and protein-RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. (
  • In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions. (
  • RNA-binding proteins (RBPs) allow cells to carry out pre-RNA processing and post-transcriptional regulation of gene expression, and aberrations in RBP functions have been linked to many diseases, including neurological disorders and cancer. (
  • However, determining the exact protein sequence regions that interact with RNA remains challenging and laborious, especially considering that many RBPs lack canonical RNA-binding domains. (
  • To benchmark our method, we identified the binding regions for polyadenylated RNA-binding proteins in HEK293 cells, allowing us to map the mRNA interaction regions of more than 1000 RBPs with very high reproducibility from replicate single-shot analyses. (
  • Two distinct families of mammalian neuron-specific RNA binding proteins (n-RBPs) have been identified as target antigens in the human paraneoplastic neurological disorders (for review, see Darnell, 1996 ). (
  • Using publicly available datasets, we identified RNA binding proteins (RBPs) with enriched motifs around the splice sites of differentially expressed circRNAs in HCC. (
  • We confirmed the binding of some of the candidate RBPs using ChIP-seq and eCLIP datasets in the ENCODE database. (
  • RNA-binding proteins (often abbreviated as RBPs) are proteins that bind to the double or single stranded RNA in cells and participate in forming ribonucleoprotein complexes. (
  • RBPs contain various structural motifs, such as RNA recognition motif (RRM), dsRNA binding domain, zinc finger and others. (
  • However, since most mature RNA is exported from the nucleus relatively quickly, most RBPs in the nucleus exist as complexes of protein and pre-mRNA called heterogeneous ribonucleoprotein particles (hnRNPs). (
  • Eukaryotic cells encode diverse RBPs, approximately 500 genes, with unique RNA-binding activity and protein-protein interaction. (
  • All RBPs bind RNA, however they do so with different RNA-sequence specificities and affinities, which allows the RBPs to be as diverse as their targets and functions. (
  • Other than core splicesome complex, RBPs also bind to the sites of Cis-acting RNA elements that influence exons inclusion or exclusion during splicing. (
  • The repertoire of RNA-binding proteins (RBPs) in bacteria play a crucial role in their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. (
  • Scientists led by Johan Auwerx's lab at EPFL, have taken a different route, and studied the link between aging and RNA-binding proteins (RBPs), which bind mRNA molecules and regulate their fate after gene transcription . (
  • PUM2 expression increases upon aging and this facilitates the capture/trapping of Mff mRNA, either alone or in association with other RNA-binding proteins (RBPs) in Ribonucleoprotein particles (RNP). (
  • In the present report we show the involvement of the RNA-binding proteins (RBPs) embryonic lethal abnormal vision (ELAV) in the regulation of HO-1 gene expression. (
  • Results: We found that similar to DNA-binding proteins (DBPs), RNA-binding proteins (RBPs) also show significantly higher values of electric moments. (
  • However, higher moments in RBPs are found to strongly depend on their functional class: proteins binding to ribosomal RNA (rRNA) constitute the only class with all three of the properties (charge, dipole and quadrupole moments) being higher than control proteins. (
  • Neural networks were trained using leave-one-out cross-validation to predict RBPs from control data as well as pair-wise classification capacity between proteins binding to various RNA types. (
  • RBPs and control proteins reached up to 78% accuracy measured by the area under the ROC curve. (
  • These changes in gene expression programs are strongly influenced by post-transcriptional mechanisms mediated by mRNA-binding factors: RNA-binding proteins (RBPs) and microRNAs (miRNAs). (
  • RBPs such as HuR (human antigen R), PTB (polypyrimidine tract-binding protein), heterogeneous nuclear ribonucleoproteins (hnRNPs), tristetraprolin, nucleolin, iron-response element-binding proteins (IRPs), and cytoplasmic polyadenylation-element-binding proteins (CPEBs), selectively bind to numerous hypoxia-regulated transcripts and play a major role in establishing hypoxic gene expression patterns. (
  • Dysregulation of RNA-binding proteins (RBPs), the key regulators of RNA processing, is one mechanism in which cancer cells select to promote tumorigenesis. (
  • We present GraphProt, a computational framework for learning sequence- and structure-binding preferences of RNA-binding proteins (RBPs) from high-throughput experimental data. (
  • RNA-binding proteins (RBPs) are key players in the post-transcriptional regulation of gene expression, regulating each step of RNA metabolism, from synthesis to decay through a dynamic association. (
  • By both polynucleotide kinase (PNK) assay and small-scale RNA interactome capture, we demonstrated, for the first time, that SDOS and TRAP1 are novel, non-canonical RBPs. (
  • The compendium of RNA-binding proteins (RBPs) has been greatly expanded by the development of RNA-interactome capture (RIC). (
  • Over 200 RBPs display differential interaction with RNA upon SINV infection. (
  • Our set includes both traditional RBPs and chromatin-associated proteins (CAPs) that lack classically defined RNA binding domains. (
  • The stability, localization and translation rate of mRNAs are regulated by a multitude of RNA-binding proteins (RBPs) that find their targets directly or with the help of guide RNAs. (
  • Binding site data for RBPs such as Argonaute 1-4, Insulin-like growth factor II mRNA-binding protein 1-3, TNRC6 proteins A-C, Pumilio 2, Quaking and Polypyrimidine tract binding protein can be visualized at the level of the genome and of individual transcripts. (
  • Almost all cellular RNAs interact with RNA-binding proteins (RBPs) to form ribonucleoprotein complexes (RNPs). (
  • RBP-RNA interactions are highly context dependent and many RBPs carry out different functions in different cellular compartments. (
  • 3 ) to predict the specificity and relative binding energy of RNA-binding proteins, computational models describing the binding specificity of RBPs (by contrast, for instance, with transcription factors) are lacking ( 4 ). (
  • These proteins include lens expressed RBPs that are identified in the iSyTE 2.0 database. (
  • RNA-binding proteins (RBPs) have roles in the regulation of many post-transcriptional steps in gene expression, but relatively few RBPs have been systematically studied. (
  • We searched for the RNA targets of 40 proteins in the yeast Saccharomyces cerevisiae: a selective sample of the approximately 600 annotated and predicted RBPs, as well as several proteins not annotated as RBPs. (
  • At least 33 of these 40 proteins, including three of the four proteins that were not previously known or predicted to be RBPs, were reproducibly associated with specific sets of a few to several hundred RNAs. (
  • Remarkably, many of the RBPs we studied bound mRNAs whose protein products share identifiable functional or cytotopic features. (
  • These results strongly suggest that combinatorial binding of RBPs to specific recognition elements in mRNAs is a pervasive mechanism for multi-dimensional regulation of their post-transcriptional fate. (
  • Diverse Combinatorial Patterns of RNA-Binding Protein Interactions with a Choice Sample of mRNAs(A-K) Putative binding sites of RBPs in target mRNAs. (
  • Putative binding sites for RBPs with strong evidence for association (1% FDR) are marked (Puf3-REFINE, Puf4-FIRE, Puf5-REFINE, Pub1-FIRE, Puf1/2-REFINE, Ssd1-REFINE, Nsr1-REFINE, Yll032c-REFINE, Pin4-REFINE, and Nrd1/Nab3-REFINE) (Figure 5 and Table S4). (
  • Background: In eukaryotic cells, RNA-binding proteins (RBPs) contribute to gene expression by regulating the form, abundance, and stability of both coding and non-coding RNA. (
  • In the vertebrate brain, RBPs account for many distinctive features of RNA processing such as activity-dependent transcript localization and localized protein synthesis. (
  • ATRBP33 shares global structural homology with all known chloroplast RBPs: a chloroplast transit peptide in the amino terminus, followed by a unique acidic domain and a tandem pair of ribonucleoprotein consensus sequence-type RNA-binding domains in the carboxyl end. (
  • Mammalian genomes encode for a large number of RNA binding proteins (RBPs), which play an important role on post-transcriptional regulation occurring during development and disease. (
  • RNA-binding proteins (RBPs) play a key role in post-transcriptional regulation of gene expression by binding to RNA along various points and at various times. (
  • as different sets of RBPs bind to the introns and exons of pre-mRNA, through splicing, polyadenylation, mRNA stabilization, nuclear transport, subcellular localization and translation. (
  • Background RNA-binding proteins (RBPs) play important roles in cellular homeostasis by controlling gene expression at the post-transcriptional level. (
  • We show that genes encoding RBPs are consistently and significantly highly expressed compared with other classes of genes, including those encoding regulatory components such as transcription factors, miRNAs and long non-coding RNAs. (
  • Analysis of the protein-protein interaction network properties for the SUR and non-SUR groups of RBPs suggests that path length distributions between SUR RBPs is significantly lower than those observed for non-SUR RBPs. (
  • We also note that RBPs exhibiting higher variability in the extent of dysregulation across breast cancer patients have a higher number of protein-protein interactions. (
  • Regulation of protein expression in neurons by controlling not only when, but where, mRNAs are translated is likely to play an important role in neuronal function. (
  • It is now clear that both processes involve mRNA-binding proteins that are primarily bound to the 3′-untranslated region (UTR) of responsive mRNAs. (
  • Although several mRNA-binding proteins that regulate mRNA transport and translation in neurons have been described, identification of the target mRNAs to which they bind has lagged behind. (
  • Logically, if protein synthesis were to occur in distinct cellular compartments, mRNAs must be identified shortly after transcription and held in a translationally dormant state during transport to the appropriate compartment. (
  • Once in the cytoplasm, these mRNA-binding proteins and their target mRNAs are packaged into granules for transport out of the cell body ( Hirokawa, 2006 ). (
  • Activity-dependent translation of localized mRNAs likely occurs via a combination of mechanisms, including activation of the general protein synthetic machinery in dendrites and release from repression of specific mRNAs. (
  • RNA-binding proteins (RBP) are involved in ( 1 ) splicing and alternative splicing of hnRNA, resulting in the formation of mRNAs. (
  • Targeted profiling of RNA translation reveals mTOR-4EBP1/2-independent translation regulation of mRNAs encoding ribosomal proteins. (
  • Alternative splicing is a mechanism by which different forms of mature mRNAs (messengers RNAs) are generated from the same gene. (
  • A protein complex immunoprecipitated by using anti-HYL1 antiserum has been reported to process miR169 pri-mRNAs into mature miRNAs ( 47 ). (
  • We found reduced expression levels of mRNAs encoding protein components of the sarcomere, the physical contractile apparatus within cardiomyocytes,' explained Dr Lara Pezzi. (
  • The outcome is the loss of the cap from mRNAs encoding sarcomere proteins, leading to their degradation and the severe contraction defects seen in SRSF3-deficient mice. (
  • The mRNAs of certain regulatory cellular proteins such as oncogenes, cytokines, lymphokines, and transcriptional activators are extremely labile. (
  • Upon its binding, PUM2 represses the translation of the target mRNAs into proteins. (
  • 2007, EMBO J, 26:2670-2681) but also by intermolecular base-pairing either between the Alu element of an mRNA 3'UTR and a partially complementary Alu element in one or more Alu element-containing long noncoding (lnc)RNAs (Gong and Maquat, 2011, Nature, 470:284-288) or between the 3'UTR Alu elements of two different mRNAs (Gong et al. (
  • In other studies, we have found that STAU1 (and probably STAU2) binding to 3'UTR inverted Alu elements competes with binding of the largely nuclear paraspeckle protein p54nrb and largely cytoplasmic protein kinase R (PKR) to mediate, respectively, the nuclear export and cytoplasmic translation of a number of mRNAs that contain these elements. (
  • Included in these studies is identifying those intramolecular and intermolecular sequences in 1/2-sbsRNAs and mRNAs that bind STAU, defining STAU-containing RNA-binding complexes, and characterizing the physiological significance of the various STAU-mediated pathways. (
  • MSI1 target mRNAs encode proteins that function in multiple pathways of cell proliferation and cell adhesion. (
  • In vivo UV-crosslinking revealed that Rrm4 binds more than 50 different mRNAs encoding cytotopically related proteins such as polarity or translation factors. (
  • RNA live imaging demonstrated that target mRNAs colocalize with Rrm4 in ribonucleoprotein particles, so-called mRNPs, that shuttle along microtubules ( 18 ). (
  • In this proposal, we aim to identify which mRNAs are direct targets of microRNAs and the RNA binding protein LIN28. (
  • 2) a large number of binding sites remain unidentified (a high false-negative rate), because CLIP-seq is sensitive to expression levels and is both time and tissue dependent [ 9 ] and (3) limited mappability [ 10 ] and mapping difficulties at splice sites lead to further false negatives, even on highly expressed mRNAs. (
  • These alterations are mainly driven by the loss of cellular mRNAs and the emergence of viral RNA. (
  • We detected widespread binding of CAPs to both lncRNAs and mRNAs, driven by a mix of gene structure and sequence composition preferences. (
  • In the cytoplasm, TIA-1 regulates the stability of mature mRNAs: its binding to AU-rich elements located in the 3′ untranslated regions (3′UTRs) of mRNAs (such as that of transforming growth factor beta, TGFβ) attracts the mRNA degradation machinery. (
  • In a particular variant of CLIP, termed PAR-CLIP (photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation), the incorporation of photo-reactive nucleotides in mRNAs prior to cross-linking induces a specific mutational signature in the sequenced reads relative to the reference genome, thereby enabling the separation of cross-linked binding sites from other RNA fragments that are captured non-specifically during the experiment ( 7 ). (
  • Termination of mRNAs is coupled to cleavage and polyadenylation while noncoding transcripts are terminated through the Nrd1-Nab3-Sen1 (NNS) pathway in a process that is linked to RNA degradation by the nuclear exosome. (
  • Saccharomyces cerevisiae RNA polymerase II (Pol II) synthesizes both mRNAs and noncoding RNAs (ncRNAs), including snRNAs, snoRNAs, and a large number of RNAs with unknown functions ( 1 , 2 ). (
  • In these cases, however, the use of alternative start sites leads to pre-mRNAs that have or do not have the Nrd1 and Nab3 binding sites in their 5′ untranslated regions (UTRs) and therefore either terminate prematurely through NNS or elongate to produce a mature mRNA. (
  • RNA localization pathways direct numerous mRNAs to distinct subcellular regions and affect many physiological processes. (
  • Despite their distinct individual properties, mutations in both the 4SN and Tsn modules mislocalize storage protein mRNAs to the cortical endoplasmic reticulum. (
  • In addition to a default pathway, two regulated pathways exemplified by the localization of rice storage protein mRNAs for prolamines and glutelins are evident. (
  • Prolamine mRNAs are targeted to the protein body (PB)-ER that delimits the prolamine intracisternal granules, whereas glutelin mRNAs are localized to the adjacent cisternal-ER. (
  • Combining RIP with quantitative real-time PCR (qRT-PCR) further enhances the RIP technique by allowing for the quantitative assessment of RNA-binding protein interactions with their target mRNAs, and how these interactions change in different cellular settings. (
  • Most interestingly, the multiple mRNAs potentially encode different polypeptides, one of which lacks a chloroplast transit peptide and acidic domain and contains only one intact RNA-binding domain. (
  • A putative RNA-binding protein positively regulates salicylic acid-mediated immunity in Arabidopsis ," Molecular Plant-Microbe Interactions , vol. 23, no. 12, pp. 1573-1583, 2010. (
  • It is important to identify which proteins can interact with RNA for the purpose of protein annotation, since interactions between RNA and proteins influence the structure of the ribosome and play important roles in gene expression. (
  • Protein-RNA interactions play significant roles in a wide range of biological processes, including regulation of gene expression, protein synthesis and replication, and the assembly of many viruses [ 1 - 4 ]. (
  • A good knowledge of protein-RNA interactions is fundamentally important for the understanding of how proteins regulate gene expression. (
  • The above reviewed papers applied a single classifier to determine the interactions between RNA and proteins. (
  • The methods available so far were subject to certain limits with regard to detecting and generally classifying RNA protein interactions which we have overcome here," Professor Vogel further. (
  • Twentyeight-Seven is building a small molecule platform to target interactions between non-coding RNAs and an emerging target class in gene regulation: RNA-binding proteins. (
  • Previously, a number of experimental methods were developed for the determination of protein-RNA interactions. (
  • These properties are regulated through modularity of a large variety of RNA-binding domains, rendering RNA-protein interactions difficult to study. (
  • We don't know the exact mechanism of how the IGF2BP3 protein interacts with the RISC complex, but it gives us a lot to investigate in terms of this interesting network of interactions," Sanford said. (
  • Protein-RNA interactions: structural characteristics and hotspot amino acids. (
  • The significance of these interactions is reflected in the recent discoveries that several human and other vertebrate genetic disorders are caused by aberrant expression of RNA-binding proteins. (
  • Here, we describe the gradient profiling by sequencing (Grad-seq) approach to draft global RNA landscapes through partitioning all cellular transcripts into diverse coding and noncoding groups based on their shared RNA-protein interactions. (
  • Here we analyze the full ensemble of cellular RNAs using gradient profiling by sequencing (Grad-seq) in the bacterial pathogen Salmonella enterica , partitioning its coding and noncoding transcripts based on their network of RNA-protein interactions. (
  • Even as they analyze the RBM45-containing stress bodies, Bowser's group is working to understand the protein and its interactions at a molecular level. (
  • Protein-RNA interactions play a central role in post-transcriptional regulation. (
  • Here I describe the development of a tool to infer the specificity of RNA binding interactions within the Rosetta framework. (
  • With a representative set of RBP interactions with single stranded RNA, the scoring functions are able to recover many of the interface side-chain dihedral angles and recapitulate the contacts involved in specific base recognition. (
  • I explore the application of the specificity prediction tools to design applications selected to illustrate a rational understanding of protein-RNA interactions and with potential therapeutic applications. (
  • Interactions involve a new motif that we call the STAU-swapping motif (SSM), and we have determined the X-ray crystal structure of the SSM of one molecule interacting with a degenerate dsRNA-binding domain of another molecule (Gleghorn et al. (
  • Background: Protein-RNA interactions play important role in many biological processes such as gene regulation, replication, protein synthesis and virus assembly. (
  • There are many outstanding questions about the molecular structures and mechanisms involved, the effects of these interactions on enzyme and RNA functions, and the factors that regulate the interactions. (
  • The effects on RNA function are likely to be wider than regulation of translation, and some enzyme-RNA interactions have been found to regulate the enzyme's catalytic activity. (
  • Several enzyme-RNA interactions have been shown to be affected by cellular factors that change under different intracellular and environmental conditions, including concentrations of substrates and cofactors. (
  • Understanding the molecular mechanisms involved in the interactions between the enzymes and RNA, the factors involved in regulation, and the effects of the enzyme-RNA interactions on both the enzyme and RNA functions will lead to a better understanding of the role of the many newly identified enzyme-RNA interactions in connecting intermediary metabolism and gene expression. (
  • the doubly shifted form may have been stabilized by protein-protein interactions. (
  • Coimmunoprecipitation (Co-IP) experiments were performed to identify the interactions between candidate molecules and their interacting proteins. (
  • Recent work has focused on better understanding RNA interactions with chromatin proteins. (
  • Here, we address this question by surveying RNA interactions of 24 proteins using the same cell type (K562) and cross-linking conditions. (
  • trp RNA-binding attenuation protein (TRAP)-trp leader RNA interactions mediate translational as well as transcriptional regulation of the Bacillus subtilis trp operon. (
  • Immunoprecipitation and subsequent isolation of nucleic acids allows for the investigation of protein:nucleic acid interactions. (
  • RNA-binding protein immunoprecipitation (RIP) is used for the analysis of protein interactions with mRNA. (
  • Although existing studies [ 7 , 9 - 24 ] have made remarkable progress to explore the interfaces of protein-RNA interactions, there is still great room for improvement. (
  • Since these proteins have the potential to affect the manner and rate of protein synthesis, it is crucial to have a reliable method for identifying and characterizing these RBP/RNA interactions. (
  • We propose that fluctuating RBP levels might result in an increase in non-specific protein interactions, potentially leading to changes in the functional consequences of RBP binding. (
  • Our analysis is a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism. (
  • RNA in cells is always associated with RNA-binding proteins that regulate all aspects of RNA metabolism including RNA splicing, export from the nucleus, RNA localization, mRNA turn-over as well as translation. (
  • RNA-binding proteins and their role in RNA metabolism: Genomic DNA is transcribed in the nucleus resulting in generation of hnRNA. (
  • Once multiple RNA targets are identified, specific features that distinguish target from non-target RNAs and the type(s) of RNA metabolism that each RBP controls can be determined. (
  • However, other domains only predict RNA binding and do not specifically indicate in which aspect of RNA metabolism they may participate. (
  • As nuclear RNA emerges from RNA polymerase, RNA transcripts are immediately covered with RNA-binding proteins that regulate every aspect of RNA metabolism and function including RNA biogenesis, maturation, transport, cellular localization and stability. (
  • How the nucleus responds to stress has been unexplored territory for ALS and other neurodegenerative disease," said Robert Bowser of the Barrow Neurological Institute in Phoenix, who presented the work at RNA Metabolism in Neurological Disease, a Society for Neuroscience satellite symposium held October 15-16 in Chicago. (
  • and a new and fascinating idea is that neurons have their own systems for regulating RNA metabolism, processing, localization, and expression ( Darnell, 2013 ). (
  • RNA binding proteins play key roles in many aspects of RNA metabolism and function, including splicing, transport, translation, localization, stability and degradation. (
  • Within the past few years, proteomics studies have identified dozens of enzymes in intermediary metabolism that bind to RNA. (
  • The wide occurrence and conservation of RNA binding ability across distant branches of the evolutionary tree suggest that these moonlighting enzymes are involved in connections between intermediary metabolism and gene expression that comprise far more extensive regulatory networks than previously thought. (
  • In light of these results a likely role for this protein in RNA metabolism during late embryogenesis and in the stress response is discussed. (
  • A specific study [ 19 ] was carried out to determine the interaction sites between RNA and Rev proteins of HIV-1 and EIAV, in which both protein-protein interface residues and protein-RNA interface residues were predicted, by first training the predictors using known protein-protein and protein-RNA complexes and then using the trained predictors to predict the binding sites of HIV-1 and EIAV Rev proteins. (
  • Translation is primarily regulated during steps one and two by complexes of proteins that interact with the mRNA. (
  • NcRNAs almost always function as ribonucleoprotein complexes and not as naked RNAs. (
  • In addition to capturing established RNA classes based on their biochemical profiles, the Grad-seq approach enabled the discovery of an overlooked large collective of structured small RNAs that form stable complexes with the conserved protein ProQ. (
  • In both cellular locations, it makes a speckled pattern consistent with the large protein/RNA complexes formed by RNA-binding proteins. (
  • Such protein-RNA complexes are resistant to the actions of denaturing and reducing agents, demonstrating very stable binding. (
  • Although many structures of various types of protein-RNA complexes have been determined, the mechanism of protein-RNA recognition remains elusive. (
  • The Rosetta-Vienna ΔΔG method is used to calculate relative binding affinities for RNA-protein complexes. (
  • Thus, these data provide evidence for widespread specific and relevant RNA association across diverse classes of chromatin-modifying complexes. (
  • In one such pathway the tumor-suppressor protein adenomatous polyposis coli (APC) targets RNAs to cell protrusions, forming APC-containing ribonucleoprotein complexes (APC-RNPs). (
  • The collection of transcripts associated with GR, identified by immunoprecipitation of GR-mRNA complexes followed by microarray analysis, revealed 479 transcripts that associated with GR. Computational analysis of the primary sequence and secondary structures of these transcripts yielded a GC-rich motif, which was shown to bind to GR in vitro. (
  • A3G associates in an RNA-dependent mechanism with multiple ribonucleoprotein (RNP) complexes and accumulates in cytoplasmic RNA-rich microdomains such as P-bodies, stress granules and Staufen-containing granules [ 23 - 26 ]. (
  • Regulation of plant innate immunity by three proteins in a complex conserved across the plant and animal kingdoms," Genes and Development , vol. 21, no. 12, pp. 1484-1493, 2007. (
  • Post-transcriptional gene regulation (PTGR) concerns processes involved in the maturation, transport, stability and translation of coding and non-coding RNAs. (
  • RNA processing is a critical component of gene expression regulation, and adaptive changes in RNA processing underlie many phenotypic differences between species. (
  • This work demonstrates that RNA regulation can be well conserved despite rapid evolution of RBP binding sites, and highlights mechanisms that may contribute to this robustness. (
  • This phenomenon is well-characterized for transcriptional regulation at promoters, but has not well been described for RNA regulation. (
  • Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. (
  • Given the strong homologies among the Hu proteins, the Drosophila neurogenic gene elav , and the Drosophila splicing factor sxl , we predict that different combinations of Hu proteins determine different neuron-specific aspects of post-transcriptional RNA regulation. (
  • In eukaryotic cells, a multitude of RNA-binding proteins play key roles in the posttranscriptional regulation of gene expression. (
  • Nevertheless, understanding of posttranscriptional regulation (a type of gene regulation) remains limited, in particular about the roles played by RNA-binding proteins (RBP) in myocardial infarction and the development of heart disease. (
  • RNA-binding proteins play important roles in post-transcriptional gene regulation by binding to specific mRNA targets. (
  • STAR (signal transduction and activation of RNA) proteins are a family of RNA-binding proteins that regulate post-transcriptional gene regulation events at various levels, such as pre-mRNA alternative splicing, RNA export, translation and stability. (
  • To gain insights into the importance of RNA regulation in embryonic stem cell self-renewal and pluripotency, we have chosen to study the RNA binding protein LIN28, one of the key genes important in stem cell biology as well as a factor in reprogramming somatic cells into induced pluripotent stem cells. (
  • Using state of the art Machine Learning techniques (such as Deep Learning architectures) the candidate will analyze Next Generation Sequencing data from various experimental methodologies (such as CLIP-Seq) in order to identify the mechanistic patterns of RNA binding protein function and regulation. (
  • However, it is unknown if these observations are specialized instances for a few key RNAs and chromatin factors in specific contexts, or a general mechanism underlying the establishment of chromatin state and regulation of gene expression. (
  • RNA-protein interaction plays an essential role in several biological processes, such as protein synthesis, gene expression, posttranscriptional regulation and viral infectivity. (
  • Therefore, identification of the RNA interacting residues in proteins provides valuable information for understanding the mechanisms of protein synthesis, gene regulation, and pathogen-host interaction. (
  • RNA binding proteins play important roles in post-transcriptional RNA processing and transcriptional regulation. (
  • RNA splicing contributes to a broad spectrum of post-transcriptional gene regulation during normal development, as well as pathological manifestation of heart diseases. (
  • Together, this study identifies regulation of RNA splicing by RBM24 as a potent player in remodeling of heart during postnatal development, and provides novel mechanistic insights to the pathogenesis of DCM. (
  • At the end of most cell signaling pathways lies a change in gene transcription or posttranscriptional regulation that affects the level or localization of protein expression. (
  • Integrated analysis of all 78 motifs reveals an unexpectedly low diversity of RNA motifs, implying frequent convergence of binding specificity towards a relatively small set of RNA motifs, many with low compositional complexity. (
  • These homologies are concentrated in three RNA recognition motifs present in all of the Hu antigens. (
  • Characterization of these proteins has led to the identification of several RNA-binding motifs, and recent experiments have begun to illustrate how several of them bind RNA. (
  • The major RNA-binding motifs are described and examples of how they may function are given. (
  • Understanding the functions of cellular transcripts based on their sequence is challenging, in particular for noncoding RNAs, which tend to lack easily recognizable motifs. (
  • A member of the ELAVL protein family, ELAV-like 3 is a neural-specific RNA-binding protein which contains three RNP-type RNA recognition motifs. (
  • Although sequence-analysis of NONA implies that it belongs to a special interspecific family of this protein type, it does contain two classical RNA recognition motifs (RRM). (
  • They especially play a major role in post-transcriptional control of RNAs, such as: splicing, polyadenylation, mRNA stabilization, mRNA localization and translation. (
  • While it lacks the prion-like low-complexity sequences of the other two proteins, it sports a nuclear localization sequence, as FUS does (see image above). (
  • In summary, RNA availability controls RBP localization and function in SINV-infected cells. (
  • Recent evidence suggests that RNA interaction can regulate the activity and localization of chromatin-associated proteins. (
  • Interestingly, Elavl2 and Igf2bp3 are shown to form a ribonucleoprotein complex with Celf1 to mediate RNA localization in vegetal cortex of Xenopus oocyte, suggesting a new direction for exploring Celf1 function in the mouse lens. (
  • ZBP is a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family of proteins that also includes hnRNP A2 and Fragile X mental retardation protein (FMRP). (
  • Diversity enabled eukaryotic cells to utilize RNA exons in various arrangements, giving rise to a unique RNP (ribonucleoprotein) for each RNA. (
  • The sequence of the encoded 16 kDa protein (MA 16) predicts that it is an RNA-binding protein, since it possesses a ribonucleoprotein consensus sequence-type RNA-binding domain (CS-RBD). (
  • Mechanistically, the protein heterogeneous nuclear ribonucleoprotein C (C1/C2) (HNRNPC) was identified to interact with KHSRP using Co-IP experiments. (
  • Synthesis of the ribosomal subunits from pre-rRNA requires a large number of trans-acting proteins and small nucleolar ribonucleoprotein particles to execute base modifications, RNA cleavages, and structural rearrangements. (
  • DEAD/DEAH box for RNA helicase activity, PAZ domain for short single-stranded RNA binding in RNAi or microRNAs (miRNA) processes, and Sm domain for snRNA binding in splicing and possibly in tRNA processing. (
  • This dual activity may depend on how the protein interacts with an important gene-silencing pathway mediated by short pieces of RNA called microRNAs. (
  • MicroRNAs can help silence gene expression by binding to messenger RNA as part of a complex known as the RNA-induced silencing complex (RISC). (
  • In some cases, IGF2BP3 may compete with microRNAs for binding sites on the messenger RNA, thereby interfering with the silencing complex. (
  • These non-coding RNAs include microRNAs, small interfering RNAs (siRNA), as well as splicesomal small nuclear RNAs (snRNA). (
  • In our proposal, we set out to solve the major problem of which genes are direct targets of microRNAs and an RNA binding protein LIN28, together they define two modes of PTC of expression in pluripotency and reprogramming. (
  • miRNAs are transcribed by RNA polymerase II as long primary transcripts, termed pri-miRNA, which are capped and polyadenylated ( 5 , 6 ). (
  • Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), to facilitate the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase. (
  • Termination of Saccharomyces cerevisiae RNA polymerase II (Pol II) transcripts occurs through two alternative pathways. (
  • To examine the effect on transcription of depleting Nab3 from the nucleus, we C-terminally tagged Nab3 with the FRB ( F KBP12- r apamycin b inding) domain in an anchor-away strain that contains an HTB (6 H is- T EV- b iotin, where TEV is tobacco etch virus) tag on the RNA polymerase subunit Rpb2 ( 15 , 40 , 41 ). (
  • Ct-RBD-1 is mainly located in the nucleolus in an RNA polymerase I transcription-dependent manner, but it is also present in discrete foci in the interchromatin and in the cytoplasm. (
  • Addition of several general RNA binding proteins, such as hnRNP A1, La autoantigen, pyrimidine tract binding protein (hnRNP I/PTB) and the major core protein of cytoplasmic mRNP (p50), rendered translation in a rabbit reticulocyte lysate cap dependent. (
  • They are cytoplasmic and nuclear proteins. (
  • In diseased neurons, this protein hangs out in cytoplasmic stress granules, a familiar compartment for scientists interested in ALS. (
  • The time course, stability, and specificity of the protein-AUUUA interaction suggests the possibility that the formation of this complex may target susceptible mRNA for rapid cytoplasmic degradation. (
  • Thus, STAU1 binding to 3'UTR inverted Alu elements, like removal of these elements by alternative RNA 3'-end cleavage and polyadenylation, obviates a PKR-mediated innate immune response to cytoplasmic 3'UTR inverted Alu elements. (
  • Instead, we show that translation occurs within cytoplasmic Fus granules leading to local protein production from APC-RNPs. (
  • These results indicate that cytoplasmic GR interacts with a subset of mRNA through specific sequences and can regulate turnover rates, suggesting a novel posttranscriptional role for GR as an RNA-binding protein. (
  • Binding of GC to the GC receptor (GR) induces its dissociation from a cytoplasmic multimeric complex of chaperone proteins and its translocation to the nucleus, where it dimerizes and acts as a transcription factor, via binding to a GC response element within the 5′ promoter region of target genes ( 4 , 5 ). (
  • Small regulatory RNA molecules are vital for salmonella and other bacteria potentially harmful to humans: This RNA type controls gene activity and allows bacteria to quickly adjust to changing conditions of living and stress as are typical during an infection, for example, when entering the blood stream or inside human cells. (
  • Professor Jörg Vogel, head of the Institute for Molecular Infection Biology of the Julius-Maximilians-Universität Würzburg (JMU) in Bavaria, Germany, is a pioneer in researching small regulatory RNA molecules. (
  • The structures of the different regulatory RNA molecules are shown left, their preferred protein binding partners on the right. (
  • New findings from Vogel's team have now been published in the journal PNAS: So far, two proteins (Hfg and CsrA) have been known to bind closely to the bacteria's regulatory RNA molecules and influence their activities. (
  • Moreover, ProQ seems to have specialised in RNA molecules with a rather complex structure. (
  • It will be particularly exciting to find out how ProQ is able to pinpoint the highly structured RNAs among millions of other RNA molecules in a cell," says Jörg Vogel. (
  • Proteins that bind to RNA molecules. (
  • A cytosolic protein was identified that binds specifically to RNA molecules containing four reiterations of the AUUUA structural element. (
  • I use the well-established knowledge-based methods trained on existing x-ray models of RBP in complex or on small molecules as well as a mixture of statistical and physical parameters used in Rosetta prediction of DNA binding proteins. (
  • This increase in repeat numbers could cause disease in several ways: the repeated segments could, for example, be transcribed into RNA molecules that soak up RNA-binding proteins and prevent these proteins from carrying out their functions ( Gitler and Tsuiji, 2016 ). (
  • PUM2 binds mRNA molecules containing specific recognition sites. (
  • In addition to using noncoding RNAs to inhibit MSI1, we are also identifying small molecules that inhibit the RNA-binding function of MSI1. (
  • Our study supports the idea of exploiting miRNAs and small molecules as novel cancer therapy targeting the RNA-binding protein, Musashi. (
  • The number of Pab1 molecules shown bound to the poly(A) tail represents the degree of enrichment of the corresponding mRNA in the Pab1 IPs (log2 immunopurification enrichment −6 = 0, −5 = 1, etc.) and not the number of Pab1 molecules bound per mRNA. (
  • Musashi-1 is a protein that binds to molecules of RNA and helps to promote cell growth during development: mice that lack this protein have serious brain defects and die shortly after birth. (
  • RNA binding motif protein 24 (RBM24) is a tissue-specific RBP which is highly expressed in human and mouse heart. (
  • Before this information can be relayed to the cytoplasm, the nascent RNA undergoes extensive post-transcriptional processing before arriving at its final destination in cells. (
  • This protein functions through post-transcriptional modification of mRNA transcripts by changing the nucleotide content of the RNA. (
  • Sxl protein could also be targeted to a new chromosomal site carrying a transgene containing splicing regulatory sequences from the Sxl gene, following transcriptional induction. (
  • The multifunctional RNA-binding protein Tudor-SN plays multiple roles in transcriptional and posttranscriptional processes due to its modular domain structure, consisting of four tandem Staphylococcus nuclease (SN)-like domains (4SN), followed by a carboxyl-terminal Tudor domain, followed by a fifth partial SN sequence (Tsn). (
  • These data define the Celf1 protein-protein interactome in the lens, in turn providing new directions for investigating RBP-based combinatorial control on the post-transcriptional level in lens development, and their relevance to cataract. (
  • Thus, we illustrate new Celf1 -regulated molecular mechanisms in lens development, suggesting that post-transcriptional regulatory RNA-binding proteins have evolved conserved functions to control vertebrate oculogenesis. (
  • RNA-binding proteins play a key role in regulating RNA processing, stability, transport, translation, and other post-transcriptional steps. (
  • I conclude that LARP1, via its RNA-mediated interaction with YB-1, is a key post-transcriptional regulator of genes involved in pre-and post-target mechanisms of cisplatin resistance. (
  • Experiments showed that the ProQ protein binds to 98 regulatory RNAs of the enterobacterial Salmonella enterica. (
  • Since the new method can basically be applied to any other organism, it is expected to provide more progress in researching regulatory RNA. (
  • Many regulatory factors control which genes get transcribed into messenger RNA and when. (
  • We confirmed that the knocking down the epithelial splicing regulatory protein 2 (ESRP2), known to be involved in the maintenance of the adult liver phenotype, significantly changed the expression of candidate circRNAs in a model HCC cell line. (
  • It is a regulatory mechanism by which variations in the incorporation of the exons into mRNA leads to the production of more than one related protein, thus expanding possible genomic outputs. (
  • Micro RNAs (miRNAs) are ≈21-nt regulatory RNAs found in viruses, plants, and animals. (
  • The splicing factor SUP-12 from Caenorhabditis elegans binds to regulatory RNA elements in pre-mRNA in order to generate tissue-specific alternative splicing for genes such as the fibroblast growth factor receptor egl - 15 . (
  • KH-type splicing regulatory protein (KHSRP) plays an important role in cancer invasion, but the relevant mechanism is not well known. (
  • In the first year of funding, we have made significant progress in elucidating the regulatory network of RNAs regulated by LIN28. (
  • These Celf1-mediated PTC outcomes depend on its interaction with other regulatory proteins. (
  • Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. (
  • Viruses have developed assorted strategies to evade A3-mediated inhibition, the most prominent of which is the expression of the dedicated regulatory protein, Vif, by most lentiviruses. (
  • In the last decade, a new picture of gene regulatory machinery has emerged, in which transcription, RNA processing, RNA stabilization, RNA export, and even aspects of translational control, are closely coupled with one another. (
  • Here we describe a streamlined proteomic workflow called peptide cross-linking and affinity purification (pCLAP) that allows rapid characterization of RNA-binding regions in proteins. (
  • The group now reports cloning and characterization of a related protein from Arabidopsis that reveals a new mechanism for hormone receptor signaling. (
  • We find that the Hu genes encode a large number of alternatively spliced transcripts to produce a series of related neuron-specific RNA binding proteins. (
  • however, some protein-encoding RNA transcripts have been shown to be subject to editing resulting in a difference in their protein's amino acid sequence. (
  • The pri-miRNAs transcripts appear to be RNA polII transcripts in plants, as they are in animals, but the hairpins are substantially more variable in length ( 26 , 27 ). (
  • The functional annotation of transcriptomes and identification of noncoding RNA (ncRNA) classes has been greatly facilitated by the advent of next-generation RNA sequencing which, by reading the nucleotide order of transcripts, theoretically allows the rapid profiling of all transcripts in a cell. (
  • By interacting with precursor and mature mRNA transcripts, RNA binding proteins (RBP) regulate the expression level and isoform of proteins within the cell in an often spatially and temporally dependent manner. (
  • Overexpression of HA epitope-tagged Rbm47 in mouse ES cells followed by RNA-binding protein immunoprecipitation, and then RT-PCR analysis of co-immunoprecipitated RNA showed that Rbm47 binds to Nanog transcript in mouse ES cells and doesn't bind to Sox2 and Oct4 transcripts in these cells. (
  • MiRNAs including miR-210, miR-373, and miR-21 associate with hypoxia-regulated transcripts and further modulate the levels of the encoded proteins to implement the hypoxic gene expression profile. (
  • RNA-binding protein that specifically bind the 3'-UTR of CDKN1A transcripts, leading to maintain the stability of CDKN1A transcripts, thereby acting as a mediator of the p53/TP53 family to regulate CDKN1A. (
  • For each protein that reproducibly bound measurable quantities of bulk RNA (90 % of the panel), we detect enrichment for hundreds to thousands of both noncoding and mRNA transcripts. (
  • The NNS complex contains two RNA-binding proteins, Nrd1 and Nab3, which recognize specific sequences in nascent transcripts and direct termination in a process that requires the RNA helicase Sen1 ( 8 , 9 , 15 - 20 ). (
  • NNS interacts with Pol II in part through binding of Nrd1 to phosphorylated Ser5 on the C-terminal domain (CTD) ( 21 - 23 ), a pattern of CTD phosphorylation most prominent in the early stages of the transcription cycle, limiting NNS termination to promoter-proximal transcripts ( 24 - 29 ). (
  • The result of this binding leads to premature termination of the majority of Nrd1 transcripts close to the 5′ end. (
  • This motif was used to predict binding of GR to an additional 7889 transcripts. (
  • LARP1 and YB-1 are both in complex with, and regulate the mRNA transcripts of genes linked to cisplatin resistance such as the efflux ATPase pump ATP7B, the DNA damage binding protein 2 (DDB2) and the pro-survival factor BCL2. (
  • Here, we used differential proteomics to show that ribosomal, mitochondrial, and cell wall-remodeling proteins, including the bacterial-type endochitinase Cts1, are differentially regulated in rrm4 Δ filaments. (
  • Across almost all characterized species, the ribosome is composed of 50 or more components that must be correctly assembled to generate a small (SSU) and a large (LSU) ribosomal subunit, each with the appropriate modifications made to the component RNA and polypeptides. (
  • For instance, the ribosome is a protein synthesis complex consisting of ribosomal RNAs (rRNAs) and proteins. (
  • There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. (
  • When a protein-coding gene is turned on, its DNA sequence gets copied into a messenger RNA molecule, which is then translated into a protein that carries out a specific function. (
  • The number of protein sequences returned does not always match the numbers of homologs shown, because the same protein sequence can be associated with multiple homologs. (
  • For mouse superfamily members not included in any HomoloGene Class, only the mouse protein sequence is returned. (
  • Some binding proteins such as neuronal specific RNA-binding proteins, namely NOVA1, control the alternative splicing of a subset of hnRNA by recognizing and binding to a specific sequence in the RNA (YCAY where Y indicates pyrimidine, U or C). These proteins then recruit splicesomal proteins to this target site. (
  • This process effectively changes the RNA sequence from that encoded by the genome and extends the diversity of the gene products. (
  • Polyadenylation is the addition of a "tail" of adenylate residues to an RNA transcript about 20 bases downstream of the AAUAAA sequence within the three prime untranslated region. (
  • Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed. (
  • p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence. (
  • The results suggest that the Rosetta scoring function may be coupled with small changes in protein sequence and structure to design specificity switches on RBP domains. (
  • The computational approach to specificity promises to improve our understanding of sequence specific binding of RNA and aid the development of protein-based approaches to target RNAs involved in disease. (
  • A list of sequences for which to calculate binding affinities relative to the sequence found in the starting structure. (
  • These can either be the full sequence of the complex (RNA and protein), or just the RNA sequence. (
  • If the protein sequence is not specified, then no mutations to the protein will be made. (
  • Here we report the side chain and backbone 1 H, 13 C and 15 N chemical shift assignments for the bacterially expressed RNA recognition motif domain from SUP-12, both in isolation as well as bound to a short RNA derived from the intron sequence between exon 4 and exon 5B of egl - 15 . (
  • These potential RNA-recognition elements were diverse in sequence, structure, and location: some were found predominantly in 3'-untranslated regions, others in 5'-untranslated regions, some in coding sequences, and many in two or more of these features. (
  • We used the keyword "RNA-binding" to search against the National Center for Biotechnology Information (NCBI) protein sequence database on June 9, 2008, and obtained 196,686 protein sequences. (
  • This protein contains six consensus RNA-binding domains and is conserved as to sequence, domain organization, and cellular location from yeast to human. (
  • A series of machine learning methods [ 6 ] such as Naive Bayes, support vector machine (SVM), and random forest (RF), combined with amino acid sequence or protein three-dimensional structural characteristics [ 4 , 7 ], have been proposed to identify RNA-binding residues. (
  • 8 ] build a neural network classifier to predict RNA-binding residues based on protein sequence and structural information. (
  • Wang and Brown [ 9 ] develop BindN, an efficient online approach that uses amino acid sequence and SVM to predict potential RNA-binding sites. (
  • 12 ] implement a RF classifier to detect the RNA binding residues in proteins by integrating interaction propensity with other sequence and structural features. (
  • We speculate that this model accounts for the broad range of retro-elements that are susceptible to repression by individual APOBEC3 proteins, and also that such substrates cannot escape APOBEC3-mediated inhibition through sequence variation. (
  • Our results show specific enrichment of many known RNA-binding regions on many known RNA-binding proteins, confirming the specificity of our approach. (
  • In nematode muscle cells, SUP-12 promotes the use of a mutually exclusive exon to impart variant binding specificity to the EGL-15 extracellular protein domain. (
  • In the new study, Sanford's team identified a set of 164 messenger RNA targets regulated by IGF2BP3 in pancreatic cancer cells. (
  • IGF2BP3 had different effects on different targets, increasing the expression of some proteins and decreasing others. (
  • These targets include mRNA, which codes for proteins, as well as a number of functional non-coding RNAs. (
  • These observations require further studies, but clearly show that RNA-binding proteins could be promising targets in aging and age-related dysfunctions. (
  • Unlike NMD, SMD detectably targets not only CBP80-CBP20-bound mRNA but also its remodeled product, eIF4E-bound mRNA (Hosoda et al. (
  • In this study, we investigated the targets of RNA-binding protein Rbm47 in mouse ES cells. (
  • Structural investigations of this STAR domain in complex with RNA have highlighted how a subset of STAR proteins specifically recognizes its RNA targets. (
  • Research by University of California, San Diego, School of Medicine scientists has demonstrated how RNA-binding proteins may represent a new class of drug target for cancers, including triple-negative breast cancer, a particularly difficult-to-treat cancer that lacks most other molecular drug targets. (
  • These data provide strong evidence that LARP4B serves as a tumor suppressor gene in glioma, encouraging further exploration of the RNA targets potentially involved in LARP4B-mediatd growth inhibition. (
  • In this award period, we completed our objective to identify other RNA targets of LIN28. (
  • A published CLIP-seq experiment for a protein of interest is available for kidney cells, but the targets of that protein are required for liver cells. (
  • We provide a solution that uses an accurate protein-binding model from the kidney CLIP-seq data, which can be used to identify potential targets in the entire transcriptome. (
  • The observation that ELAVL3 is one of several Hu antigens (neuronal-specific RNA-binding proteins) recognized by the anti-Hu serum antibody present in sera from patients with paraneoplastic encephalomyelitis and sensory neuronopathy (PEM/PSN) suggests it has a role in neurogenesis. (
  • The transcribed RNA now represents information required to direct cellular function to maintain cell homeostasis. (
  • We found that CPEB1, one of a family of hundreds of RNA-binding proteins in the human genome, is important for establishing productive cytomegalovirus infections," said senior author Gene Yeo, PhD, professor of cellular and molecular medicine at UC San Diego School of Medicine. (
  • More than 200 cellular RNA-binding proteins change their binding activity in response to this challenge, mainly driven by transcript availability. (
  • Double-stranded RNA (dsRNA) produced during viral infection activates several cellular antiviral responses ( 31 , 36 , 42 , 47 ). (
  • We show that both proteins bind to multiple different RNAs, including viral RNA as well as cellular coding and non-coding RNAs, with relatively little evidence of selectivity. (
  • Specifically, HIV-1 Vif counteracts APOBEC3 proteins by inducing their proteasomal degradation through the direct recruitment of CBF-β and a cellular E3 ubiquitin ligase comprising CUL5, ELOB/C, and RBX2 [ 12 - 15 ]. (
  • type proteasome subunit and a transformer-2-like SR-related protein: early induction of the corresponding genes in tobacco cells treated with cryptogein," Plant Molecular Biology , vol. 35, no. 3, pp. 261-269, 1997. (
  • It's basically a little molecular machine with a guidance system made of microRNA, and it silences genes by blocking translation of the messenger RNA," Sanford said. (
  • Using genomics technologies, the researchers also found that increased CPEB1 levels in CMV-infected cells leads to abnormal processing of RNAs encoding thousands of human genes. (
  • Initial annotation ( 1 ) indicated that the human genome contains ~300 genes that encode proteins with an RNA-recognition motif (RRM). (
  • We have extended these analyses to another member of the β subfamily of herpesviruses, murine cytomegalovirus (MCMV), and now report that products of the m142 and m143 genes together bind dsRNA. (
  • Like the human cytomegalovirus dsRNA-binding protein genes TRS1 and IRS1, m142 and m143 are members of the US22 gene family. (
  • Here, we report the identification of two such genes, m142 and m143, the products of which bind dsRNA and rescue replication of VVΔE3L. (
  • We report that a conserved RNA-binding protein Celf1 post-transcriptionally controls key genes to regulate lens fiber cell differentiation. (
  • FCA functions with a protein partner known as FY, and in vitro binding assays showed that binding of ABA to FCA disrupted the interaction of FCA and FY. (
  • To analyze the interaction network of the RBPome and thus to find all binding sites of a specific RBP, a CLIP-seq experiment is only the initial step. (
  • This interdisciplinary bioinformatics project touches on Machine Learning for pattern recognition, Next Generation Sequencing Analysis, and Protein-RNA Interaction Networks. (
  • However, experimental determination of RNA-protein interaction remains time-consuming and labor-intensive. (
  • The proposed method can be used in other research areas, such as DNA-binding site prediction, protein-protein interaction, and prediction of posttranslational modification sites. (
  • The prediction results of RNA-binding sites in proteins can provide biological insights for investigating RNA-protein interaction. (
  • no single feature can effectively identify protein-RNA interaction residues. (
  • Upon cisplatin treatment, the interaction of LARP1 with YB-1 was preserved only in the resistant cell line and was further investigated as both proteins are known for promoting cisplatin resistance. (
  • This region of chromosome 22 encodes the N-terminal transactivation domain of the EWS protein and that region may become joined to one of several other chromosomes which encode various transcription factors, see The expression of a chimeric protein with the EWS transactivation domain fused to the DNA binding region of a transcription factor generates a powerful oncogenic protein causing Ewing sarcoma and other members of the Ewing family of tumors. (
  • The normal EWS gene encodes an RNA binding protein closely related to FUS (gene) and TAF15, all of which have been associated to amyotrophic lateral sclerosis. (
  • The mRNA encodes for a protein called mitochondrial fission factor (MFF), and is a pivotal regulator of mitochondrial fission-a process by which mitochondria break up into smaller mitochondria. (
  • These results reveal that MCMV, like many other viruses, encodes dsRNA-binding proteins, at least two of which can inhibit dsRNA-activated antiviral pathways. (
  • A gene on chromosome Xp11.23 that encodes a nuclear protein of the RNA-binding motif family of currently unknown function. (
  • In eukaryotic cells, synthesis of most proteins is driven by cap-dependent mRNA translation ( Sonenberg and Dever, 2003 ). (
  • In eukaryotic cells, miRNAs and piRNAs are the most common small RNAs that mediate gene silencing. (
  • Select one or more mouse PIRSF members to download protein sequences or forward to NCBI BLAST. (
  • You can select a given mouse superfamily member and download (or forward to NCBI BLAST) FASTA formatted protein sequences of that mouse gene and its mouse, human and rat homologs, as defined in the corresponding HomoloGene Class. (
  • You can also "Select all" mouse superfamily members to obtain their protein sequences and the protein sequences for all mouse, human and rat homologs of the mouse superfamily members. (
  • The scoring function is able to largely recapitulate the results of experimentally investigated mutations of the pumilio-1 domain being investigated as a universal platform for binding arbitrary RNA sequences specifically. (
  • Unexpectedly, the mRNA sequences were still dysregulated in more than half of the samples: if there was no repeat RNA to trap hnRNP H, how could this be the case? (
  • Although numerous binding sites were also identified in intronic sequences, our RNA transcriptome sequencing analysis does not favor the idea that MSI1 is a major regulator of splicing in glioblastoma cells. (
  • This is a text file specifying the sequences for which we want to calculate relative binding affinities. (
  • Do not do the Vienna RNAfold calculations (i.e. assume the folding free energy of all RNA sequences is 0). (
  • The protein did not appear to recognize either branch point or AG dinucleotide sequences, but an adenosine residue at the 5' end of the poly(U) tract enhanced binding severalfold. (
  • In recent years, rapid advances in genomic and proteomic studies have yielded a tremendous amount of DNA and protein sequences. (
  • 10 , 11 ] propose a Naive Bayes classifier named RNABindR that can predict RNA-binding amino acids from 3D protein structures or protein sequences of unknown structure are most likely to interact with RNA. (
  • In this review I focus on the mRNA-binding proteins that control mRNA translation in neurons and how they may participate in local, synaptodendritic protein synthesis. (
  • That protein synthesis may occur outside the neuronal cell body was first suggested in the early 1980s by the finding that polyribosomes are localized to subsynaptic regions ( Steward and Levy, 1982 ). (
  • Of the potential functional significance for local protein synthesis, Steward and Levy (1982) wrote, "It is difficult to conceive of a situation which is intuitively more appealing as a mechanism for protein synthesis-dependent maintenance or modification of a synapse as a function of the activity over that synapse. (
  • Indeed their excitement was shared by many researchers who, over the next decade, characterized the dendritic presence of the molecular machinery required for protein synthesis. (
  • This review focuses on RNA-binding proteins and their role in regulating local protein synthesis in neurons. (
  • Among these are the protein kinase R and oligoadenylate synthetase/RNase L pathways, both of which result in the shutoff of protein synthesis. (
  • Many viruses, including human cytomegalovirus, encode dsRNA-binding proteins that prevent the activation of these pathways and thereby enable continued protein synthesis and viral replication. (
  • Among the best characterized of these is the shutoff of protein synthesis mediated by protein kinase R (PKR) and oligoadenylate synthetase (OAS)/RNase L. Since viral replication depends on protein synthesis, many viruses have evolved mechanisms for counteracting the PKR and OAS/RNase L pathways ( 36 ). (
  • Infection with VV lacking the E3L gene (VVΔE3L) results in activation of the PKR and OAS/RNase L pathways, shutoff of protein synthesis, little or no viral replication in most cell types, and very reduced virulence in infected animals ( 2 - 4 , 9 , 27 ). (
  • report that m142 and m143 are each necessary to block PKR activation and enable ongoing protein synthesis necessary for MCMV replication ( 43 ). (
  • Budding yeast, for example, can produce 2000 ribosomes per minute [ 1 ], reflecting the demands of protein synthesis. (
  • Using the Surface Sensing of Translation (SUnSET) method, LARP1 was found to play a fundamental role in maintaining protein synthesis during genotoxic stress. (
  • Furthermore, it plays a vital role in preserving "de novo" protein synthesis and consequently cell survival during cisplatin induced genotoxic stress. (
  • For this process the RNA is associated with nuclear proteins that aid in splicing and nuclear export [ 1 ]. (
  • The Arabidopsis protein is known as FCA and is a nuclear RNA-binding protein that functions by preventing the accumulation of an mRNA that represses flowering. (
  • Human nuclear RNAi-defective 2 (NRDE2) is an essential RNA splicing factor. (
  • Bowser and colleagues observed that while the protein appears to be predominantly nuclear, some collects in the cytoplasm. (
  • In contrast, a presumptive small nuclear RNP protein was observed at several heat puffs following shock. (
  • SDOS, also known as Nudt16l1, is a paralog of the catalytic nuclear Nudt16p family of proteins that has been predicted to lack the decapping activity. (
  • In this study, we validated and characterized the binding event between hit compounds and MSI1 RNA-binding domain 1 (RBD1) using nuclear magnetic resonance. (
  • This process uses mitoribosomes that contain 80 protein components that are nuclear-encoded, translated in the cytosol and then imported into the organelle. (
  • The RNA-binding protein Celf1 post-transcriptionally regulates p27Kip1 and Dnase2b to control fiber cell nuclear degradation in lens development. (
  • An Arabidopsis cDNA (Atrbp33) encoding a nuclear-encoded chloroplast RNA-binding protein (RBP) has been isolated (A.J.DeLisle [1993] Plant Physiol 102: 313-314). (
  • Among them we confirmed TMEM107, a ciliary transition zone protein, as directly bound at RNA level by SDOS, as demonstrated by RNA-immunoprecipitation analysis. (
  • Here, we perform formaldehyde RNA immunoprecipitation (fRIP-Seq) to survey the RNA associated with a panel of 24 chromatin regulators and traditional RNA binding proteins. (
  • We refined a formaldehyde cross-linking RNA immunoprecipitation technique followed by deep sequencing (fRIP-Seq) to perform triplicate experiments that showed high concordance, exceeding previous genome-wide surveys of individual CAPs. (
  • Among the experimental methods for mapping RBP binding sites, cross-linking and immunoprecipitation (CLIP) coupled with deep sequencing provides transcriptome-wide coverage as well as high resolution. (
  • Immunoprecipitation (IP) was performed with Celf1-specific antibody (test) or IgG (control) on protein lysates prepared from embryonic day (E) 16.5 and early post-natal day (P) 5 wild-type mouse lens, and the mouse lens epithelium-derived cell line 21EM15. (
  • Here, we describe the immunoprecipitation of the RNA-binding protein AUF1 with several different factors associated with the senescence-associated secretory phenotype (SASP) (Alspach and Stewart, 2013), specifically IL6 and IL8. (
  • Using immunoprecipitation followed by ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) in cisplatin sensitive (OVCAR3) and resistant (OVCAR8) ovarian cancer cell lines before and after cisplatin treatment, I identified PABP1, and YB-1 as strong, RNA-dependent LARP1 interactors in both cell lines. (
  • Staufen1 and 2 represent the other conserved family of RNA-binding proteins with demonstrable roles in mRNA transport in neurons. (
  • To elucidate the biochemical mechanism of miRNA processing, we developed an in vitro miRNA processing assay using purified recombinant proteins. (
  • DCL1 and HYL1 recombinant proteins form a complex in vitro ( 43 , 44 ), and HYL1 has been reported to interact with SE ( 45 ). (
  • RNA binding by Sxl proteins in vitro and in vivo. (
  • We have therefore examined the RNA-binding properties of Sxl protein in vitro and in vivo. (
  • A major qualitative difference between CLIP-seq and RNAcompete data is that the latter determines relative binding affinities in vitro , whereas CLIP-seq detects binding events in vivo . (
  • In the dipteran Chironomus tentans, RBD-1 (Ct-RBD-1) binds pre-rRNA in vitro and anti-Ct-RBD-1 antibodies repress pre-rRNA processing in vivo. (
  • Future studies aim to elucidate how mammalian cells utilize STAU and other dsRNA-binding proteins to regulate gene expression. (
  • HO-1 is a heat shock protein (HSP32) and it is recognized as one of the major stress-inducible protein in mammalian cells ( Maines, 1997 ). (
  • In response to hypoxic challenge, mammalian cells mount a well-orchestrated response that includes specific changes in the collective of expressed proteins. (
  • Asymmetric segregation of the double-stranded RNA binding protein Staufen2 during mammalian neural stem cell divisions promotes lineage progression. (
  • An Asymmetrically Localized Staufen2-Dependent RNA Complex Regulates Maintenance of Mammalian Neural. (
  • The selection step would be expected to occur at an early time after transcription, so that these messages would be sequestered from the vast protein synthetic machinery located within the cell body. (
  • Less well understood are RNA binding proteins, such as IGF2BP3, which interact with the messenger RNA itself to regulate gene expression after transcription has occurred. (
  • Changes in transcription directly affect the abundance of some hypoxia-regulated proteins. (
  • For example, Nrd1 autoregulates its own transcription by binding, along with Nab3, to sites in the 5′ end of its nascent pre-mRNA ( 9 , 36 ). (
  • When Vif is absent or defective, APOBEC3 proteins are packaged into progeny virions and transferred to target cells during new infections, where they inhibit reverse transcription and hypermutate nascent cDNAs through excessive cytidine-to-uridine editing [ 5 , 7 , 16 - 19 ]. (
  • This paper tries to identify proteins that can interact with RNA using voting systems. (
  • Coimmunoprecipitation experiments demonstrate that these two proteins interact in infected cells, consistent with their previously reported colocalization. (
  • Based on these and other results, we suggest that one function of general mRNA binding proteins in the cytoplasm is to promote ribosome binding by a 5' end, cap-mediated mechanism, and prevent spurious initiations at aberrant translation start sites. (
  • Uncharacterized mRNA-binding proteins are plentiful in plants and animals, and the findings suggest that some of these could be hormone receptors. (
  • p>This subsection of the 'Names and Taxonomy' section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein. (
  • The recent development of massive-scale messenger RNA (mRNA) sequencing technology has permitted the identification of gene expression patterns associated with the development of heart disease. (
  • Recently, however, experimental methods for high-throughput and high-resolution identification of RBP binding sites have been developed. (
  • Identification of RNA-binding sites in proteins provides valuable insights for biologists. (
  • The nod-encoded polypeptide is inferred to bind single-stranded nucleic acids. (
  • Moreover, physicochemical properties and amino acid preferences of RNA-binding proteins are examined and analyzed. (
  • In doing so we have performed a genome-wide nucleotide-level resolution map of LIN28 binding sites in messenger RNAs in human embryonic stem cells and somatic cells expressed a tagged version of LIN28. (
  • RNA-binding protein Rbm47 binds to Nanog in mouse embryonic stem cells. (
  • Celf1-IP coupled with MS/MS-based proteomic analysis identified potential new Celf1-binding proteins in embryonic, postnatal mouse lens and 21EM15 cell line. (
  • S. van Nocker and R. D. Vierstra, "Two cDNAs from Arabidopsis thaliana encode putative RNA binding proteins containing glycine-rich domains," Plant Molecular Biology , vol. 21, no. 4, pp. 695-699, 1993. (
  • Basic binding mechanism of a putative RNA-binding protein (HI1333 from Haemophilus influenza) is suggested as a potential application of this study. (
  • Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA. (
  • Some investigations code a protein using primary amino acid compositions [ 10 , 11 , 13 , 14 ], and some code with protein chemical or physical properties and structural information [ 10 - 12 , 14 - 16 ]. (
  • 21 ] proposed a few voting systems for the classification (prediction) of protein structural classes. (
  • I know of no existing computational method that infers base binding probabilities from structural models. (
  • The present review focuses on the structural basis of RNA recognition by this family of proteins. (
  • We further calculate the feature importance of different feature categories and find that structural neighborhood characteristics are critical in the recognization of RNA binding residues. (
  • Distinguishing the RNA-binding residues in proteins is crucial for understanding how protein and RNA recognize each other and function together as a complex. (
  • They found that most of the targeted RNAs encode proteins that have some role in cancer biology, such as cell migration, proliferation, and adhesion. (
  • The Hu family of proteins was identified as target antigens in a paraneoplastic neurological syndrome (the Hu syndrome) consisting of a diverse set of neuronal degenerations associated with small-cell lung cancer. (
  • Messenger RNAs are then transported from nucleus into the cytoplasm ( 2 ). (
  • The results of genetic studies in Arabidopsis indicate that three proteins, the RNase III DICER-Like1 (DCL1), the dsRNA-binding protein HYPONASTIC LEAVES1 (HYL1), and the C2H2 Zn-finger protein SERRATE (SE), are required for the accurate processing of microRNA (miRNA) precursors in the plant cell nucleus. (
  • The class II RNase III Drosha, together with the dsRNA-binding protein (dsRBP) DGCR8/Pasha, cleaves the stem loop of pri-miRNA in the nucleus to a hairpin RNA (pre-miRNA) of ≈70 nt ( 8 - 11 ). (
  • The pre-miRNAs are transported out of the nucleus by the Ran-binding protein exportin 5 ( 12 - 14 ). (
  • In a previous eLife paper, researchers at Columbia University reported that one of these proteins, called hnRNP H, attaches to the repeat RNA in C9orf72 and forms clumps within the nucleus. (
  • In human cells, RNA is the genetic material that carries instructions from the DNA in a cell's nucleus out to the cytoplasm, where molecular machinery uses those instructions to build proteins. (
  • We propose a method, RNAProB, which incorporates a new smoothed position-specific scoring matrix (PSSM) encoding scheme with a support vector machine model to predict RNA-binding sites in proteins. (
  • Developing computational methods to predict RNA-binding sites precisely is becoming increasingly important. (
  • Here, we report that human ribosome-binding factor A (RBFA) is a mitochondrial RNA-binding protein that exerts crucial roles in mitoribosome biogenesis. (
  • In comparison, eubacterial ribosome biogenesis appears to require relatively few factors, with GTPases being well represented among the 20 or so proteins that are known to be required [ 6 , 7 ]. (
  • We have characterized a novel protein, RNA-binding domain-1 (RBD-1), that is involved in ribosome biogenesis. (
  • Then simple majority voting system (SMVS) is used for the prediction of RNA-binding proteins, achieving average ACC (overall prediction accuracy) value of 79.72% and MCC (Matthew's correlation coefficient) value of 59.77% for the independent testing dataset. (
  • Thus, computational approaches for prediction of RNA-binding sites in proteins have become highly desirable. (
  • Extensive studies of RNA-binding site prediction have led to the development of several methods. (
  • Our results demonstrate that smoothed PSSM encoding scheme significantly enhances the performance of RNA-binding site prediction in proteins. (
  • The superior performance over existing RNA-binding residue prediction methods indicates the importance of the gradient tree boosting algorithm combined with the optimal selected features. (
  • Using a systems genetics approach, the researchers then identified a new mRNA target that PUM2 binds. (
  • By understanding the systemic changes in transcriptome splicing, we can identify new proteins involved in the molecular pathways leading to HCC development and progression. (
  • Most of these proteins are regulated by signalling pathways through post-translational modifications, such as phosphorylation and arginine methylation. (
  • RNA-Binding Protein Musashi1 Is a Central Regulator of Adhesion Pathways in Glioblastoma. (
  • We have found that STAU1, which is a double-stranded RNA binding protein, recruits the NMD factor UPF1 to certain mRNA 3'-untranslated regions (3'UTRs) so as to elicit SMD in a translation-dependent mechanism (reviewed in Park and Maquat, 2013, Wiley Interdiscip Rev RNA 4:423-435). (
  • In response to viral infection, cells activate a variety of antiviral responses, including several that are triggered by double-stranded (ds) RNA. (
  • Here, we show that the double-stranded RNA-binding protein Stau2 is distributed asymmetrically during progenitor divisions in the developing mouse cortex, preferentially segregating into the Tbr2(+) neuroblast daughter, taking with it a subset of RNAs. (
  • RISC is comprised of Argonaute (Ago) proteins and accessory RNAs, and mediates mRNA degradation by complementary small double-stranded RNAs. (
  • New findings from Sanford's lab at UC Santa Cruz, where he is an associate professor of molecular, cell, and developmental biology, point toward a possible mechanism by which this protein drives metastasis. (
  • The same mechanism is conserved also in the nematode C. elegans, where the protein PUF-8 is also induced upon aging. (
  • These results help in understanding the mechanism of protein-RNA recognition, and identifying RNA-binding proteins. (
  • One such mechanism is the sequestration of dsRNA by a viral dsRNA-binding protein, such as pE3L, the product of the vaccinia virus (VV) E3L gene ( 22 ). (
  • The mechanism of APOBEC3 virion packaging awaits elucidation, though a dependency on RNA binding has been established. (
  • Thus, the encapsidation of APOBEC3 proteins into viral particles is essential for their antiviral activity, and a complete description of APOBEC3 protein function will require a full understanding of the packaging mechanism. (
  • Especially during development and differentiation, ncRNAs provide a finely tuned mechanism for lineage-specific or even cell-specific protein expression. (
  • An important control point in gene expression is at the level of messenger RNA (mRNA) stability. (
  • In addition, they were surprised to find that CPEB1 was necessary for proper processing of viral RNAs. (
  • Without the host CPEB1 protein, viral RNA did not mature properly and the virus was weakened. (
  • Yeo said the next steps are to determine the therapeutic value of inhibiting CPEB1 in CMV infections and identify other RNA-binding proteins that may be important in other viral infections. (
  • Many of these RNA-binding proteins regulate viral replication and can be targeted to influence infection outcome. (
  • The Ebola virus VP35 protein binds viral immunostimulatory and host RNAs identified through deep sequencing. (
  • yet, there are no data that identify viral immunostimulatory RNAs (isRNA) or host RNAs bound to VP35 in cells. (
  • Utilizing a SeV infection model, we demonstrate that both viral isRNA and host RNAs are bound to Ebola and Marburg VP35s in cells. (
  • In contrast to other well-characterized viral dsRNA-binding proteins, m142 and m143 act in a complex to bind dsRNA and rescue VVΔE3L replication. (
  • Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Ave, New York 10065, USA. (
  • Mitochondrial RNA-binding proteins, molecular model. (
  • In this context, we investigated the role played by TRAP1, a molecular chaperone whose role in cancer has been extensively described, and its predicted interacting-partner Protein Syndesmos (SDOS). (
  • However, when searching against Protein Data Bank (PDB) [ 4 ] for molecular/chain type containing protein and RNA, we only retrieved 684 structures. (
  • For each protein, we find that the enriched sets of RNAs share distinct biochemical, functional, and chromatin properties. (
  • This is only one of the over 40 distinct protein domains known to contact RNA. (
  • Given their diverse functions, cells express a variety of RNA-binding proteins, which play important roles in the pathologies of a number of diseases. (
  • 1 ] applied predicted RNA-binding sites to study the relationship between RNA methyltransferases RsmC and 16S rRNA. (
  • The generic nature of the Grad-seq approach will help to rapidly describe functional RNA landscapes in numerous understudied microbes. (