RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.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)Molecular Sequence Data: 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.Ribonucleoproteins: Complexes of RNA-binding proteins with ribonucleic acids (RNA).Hu Paraneoplastic Encephalomyelitis Antigens: 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.Protein Binding: 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, Messenger: 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.Amino Acid Sequence: 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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Heterogeneous-Nuclear Ribonucleoproteins: 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.RNA Stability: 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.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Poly(A)-Binding Proteins: 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.RNA Processing, Post-Transcriptional: 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.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.RNA, Small Interfering: 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.RNA, Double-Stranded: 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.RNA Editing: 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).Protein Structure, Tertiary: 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.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Nuclear Factor 90 Proteins: 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.HeLa Cells: 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.RNA Helicases: A family of proteins that promote unwinding of RNA during splicing and translation.Mutation: 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.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Nuclear Proteins: 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.Angiomyoma: A benign tumor consisting of vascular and smooth muscle elements.DNA-Binding Proteins: 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.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.RNA Interference: 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.Heterogeneous-Nuclear Ribonucleoprotein Group A-B: 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.RNA, Ribosomal: 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)RNA Precursors: 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.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Nematospiroides: A genus of nematodes found mainly in mice. Its organisms are used in biomedical research.Nanoarchaeota: A kingdom of hyperthermophilic ARCHAEA found in diverse environments.Nuclear Factor 45 Protein: A protein subunit that takes part in forming nuclear factor 90 protein complexes.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Gene Expression Regulation: 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.Amino Acid Motifs: 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.Conserved Sequence: 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.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Recombinant Fusion Proteins: 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.DNA-Directed RNA Polymerases: 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).Escherichia coli: 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.Heterogeneous-Nuclear Ribonucleoprotein D: 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).Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Cytoplasm: 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)Cloning, Molecular: 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.Polypyrimidine Tract-Binding Protein: 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.RNA-Binding Protein FUS: 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.Saccharomyces cerevisiae Proteins: 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.Immunoprecipitation: 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.Sequence Alignment: 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.RNA, Protozoan: Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.RNA, Chloroplast: Ribonucleic acid in chloroplasts having regulatory and catalytic roles as well as involvement in protein synthesis.Saccharomyces cerevisiae: 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.Alternative Splicing: 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.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.Drosophila Proteins: 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.RNA Polymerase II: 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 2.7.7.6.mRNA Cleavage and Polyadenylation Factors: Factors that are involved in directing the cleavage and POLYADENYLATION of the of MESSENGER RNA near the site of the RNA 3' POLYADENYLATION SIGNALS.Polyadenylation: 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.RNA, Small Nuclear: 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.MicroRNAs: 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.Host Factor 1 Protein: 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.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Retinol-Binding Proteins: Proteins which bind with RETINOL. The retinol-binding protein found in plasma has an alpha-1 mobility on electrophoresis and a molecular weight of about 21 kDa. The retinol-protein complex (MW=80-90 kDa) circulates in plasma in the form of a protein-protein complex with prealbumin. The retinol-binding protein found in tissue has a molecular weight of 14 kDa and carries retinol as a non-covalently-bound ligand.Protein Conformation: 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).DEAD-box RNA Helicases: 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.RNA Viruses: Viruses whose genetic material is RNA.Heterogeneous-Nuclear Ribonucleoprotein Group C: 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, Untranslated: 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.RNA Transport: The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.Two-Hybrid System Techniques: 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.RNA, Nuclear: RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Poly(A)-Binding Protein I: 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.Viral Proteins: Proteins found in any species of virus.Tacrolimus Binding Proteins: A family of immunophilin proteins that bind to the immunosuppressive drugs TACROLIMUS (also known as FK506) and SIROLIMUS. EC 5.2.1.-Models, Biological: 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.Repressor Proteins: 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.RNA, Guide: 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.5' Untranslated Regions: 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.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Promoter Regions, Genetic: 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.Nucleocytoplasmic Transport Proteins: 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.Ribonuclease III: 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.Untranslated Regions: The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.DNA, Complementary: 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.DNA: 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).Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.RNA, Catalytic: 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.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Nerve Tissue ProteinsTristetraprolin: 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.Kinetics: The rate dynamics in chemical or physical systems.DNA Primers: 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.Blotting, Western: 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.Iron-Regulatory Proteins: 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.Exons: 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.Transfection: 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.Oligoribonucleotides: 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.Bacterial Proteins: Proteins found in any species of bacterium.Zinc Fingers: 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.Consensus Sequence: 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.RNA Caps: 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.Regulatory Sequences, Ribonucleic Acid: Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.Reverse Transcriptase Polymerase Chain Reaction: 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.Ribosomal Proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.Molecular Weight: The sum of the weight of all the atoms in a molecule.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)RNA Folding: The processes of RNA tertiary structure formation.RNA, Antisense: 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.Insulin-Like Growth Factor Binding Proteins: 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)Introns: 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.Poly A: 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.Protein Isoforms: Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.Cells, Cultured: 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.Electrophoretic Mobility Shift Assay: 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.Fragile X Mental Retardation Protein: 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.RNA, Transfer: 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.Xenopus Proteins: 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.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Plasmids: 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.Ribonucleoproteins, Small Nuclear: 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).Arctostaphylos: A plant genus of the family ERICACEAE.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.RNA, Helminth: Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.Ribosomes: Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.Polyribosomes: 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)Spliceosomes: 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.Trypanosoma brucei brucei: 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).Protein Transport: 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.Cross-Linking Reagents: 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.Virus Replication: 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.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Blotting, Northern: 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.Protozoan Proteins: Proteins found in any species of protozoan.Genes, Reporter: 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.Fatty Acid-Binding Proteins: 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.Arabidopsis: 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.Binding, Competitive: 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.Active Transport, Cell Nucleus: Gated transport mechanisms by which proteins or RNA are moved across the NUCLEAR MEMBRANE.Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.Drosophila: 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.Gene Expression Regulation, Developmental: 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.Proteins: 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.Signal Transduction: 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.Caenorhabditis elegans Proteins: 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.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Sequence Homology, Nucleic Acid: 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.Cell Line, Tumor: A cell line derived from cultured tumor cells.HEK293 Cells: A cell line generated from human embryonic kidney cells that were transformed with human adenovirus type 5.Gene Deletion: 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.Green Fluorescent Proteins: 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.Alcohol Deterrents: Substances interfering with the metabolism of ethyl alcohol, causing unpleasant side effects thought to discourage the drinking of alcoholic beverages. Alcohol deterrents are used in the treatment of alcoholism.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Fungal Proteins: Proteins found in any species of fungus.Caenorhabditis elegans: A species of nematode that is widely used in biological, biochemical, and genetic studies.Poly(A)-Binding Protein II: 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.Ultraviolet Rays: 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.Point Mutation: 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.Calcium-Binding Proteins: Proteins to which calcium ions are bound. They can act as transport proteins, regulator proteins, or activator proteins. They typically contain EF HAND MOTIFS.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Protein Structure, Secondary: 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.Adaptor Proteins, Signal Transducing: 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 enzymesGene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.eIF-2 Kinase: 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.Polymerase Chain Reaction: 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.Argonaute Proteins: 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.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Periplasmic Binding Proteins: 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.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Models, Genetic: 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.Xenopus: An aquatic genus of the family, Pipidae, occurring in Africa and distinguished by having black horny claws on three inner hind toes.Insulin-Like Growth Factor Binding Protein 3: 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.Protein Interaction Mapping: Methods for determining interaction between PROTEINS.Oogenesis: The process of germ cell development in the female from the primordial germ cells through OOGONIA to the mature haploid ova (OVUM).Karyopherins: 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.In Situ Hybridization: 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.Down-Regulation: 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.RNA, Heterogeneous Nuclear: 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.Gene Knockdown Techniques: 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.Oocytes: 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).Cytoplasmic Granules: Condensed areas of cellular material that may be bounded by a membrane.RNA, Neoplasm: RNA present in neoplastic tissue.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Ribonucleoprotein, U1 Small Nuclear: 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.Oligonucleotide Array Sequence Analysis: 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.Levivirus: A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.HIV-1: The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.TATA-Box Binding Protein: 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.
This attachment is mediated by the phage's receptor binding protein (RBP), which recognizes and binds to a receptor on the ... RBPs are also referred to as host-specificity protein, host determinant, and antireceptor. For simplicity, the RBP term will be ... Silva Comprehensive Ribosomal RNA Database. Retrieved 2012-05-17. Mc Grath S and van Sinderen D (editors). (2007). ... Analysis of the crystal structure of several RBPs indicates that these proteins share a common tertiary folding, and support ...
Even though protein with DNA binding domains are more abundant than protein with RNA binding domains, a recent study by Cheadle ... For Drosophila RBPs associated with splicing or nonsense mediated decay, analyses of protein-protein and protein-RNA ... In fact several key genes such as nanos are known to bind RNA but often their targets are unknown. Although RNA binding ... Poly(A)-binding protein (PABP) binds to a long poly(A) tail and mediates the interaction between EIF4E and EIF4G which ...
Potential roles include the following: Binding to RNA-binding proteins (RBPs) and RNAs besides miRNAs to form RNA-protein ... 2013: Tested natural circRNAs that contained a translation "start codon." However, none of these molecules bound to ribosomes, ... Many circular RNAs arise from otherwise protein-coding genes. They have been categorized as noncoding RNA, but more recently, ... Argonaute proteins are the "effector proteins" which help miRNAs carry out their job, while microRNA sponges are RNAs that " ...
RNA-binding proteins ( RBPs ) play critical role during this process. All RBPs can bind to RNA depends on different ... a database for RNA-binding proteins. Protein-RNA interface: a database for Protein-RNA interface. Rice RNA Binding Protein ... As the result, RBPs can bind RNA with higher specificity and affinity than single domain. RNA-binding protein database has ... RBPs contain at least one RNA-binding domains and usually they have multiple binding domains. RNA-binding domain (RBD, also ...
RNA-binding proteins (often abbreviated as RBPs) are proteins that bind to the double or single stranded RNA in cells and ... RNA-binding protein database starBase platform: a platform for decoding binding sites of RNA binding proteins (RBPs) from large ... identification of RNA-binding proteins has extended the number of RNA-binding proteins significantly RNA-binding protein Sam68 ... intricacy of protein-RNA recognition of RRM as it entails RNA-RNA and protein-protein interactions in addition to protein-RNA ...
... or RNA-binding proteins (RBPs). Similarly, competition by ceRNAs for RNA-binding proteins has also been reported in eukaryotic ... Several of these HSURs are able to bind to and compete for three host-cell microRNAs and thus regulate host-cell gene ... CREB (cAMP response element binding protein) has been implicated in the upregulation of HULC. HULC RNA inhibits miR-372 ... These competitive endogenous RNAs (ceRNAs) act as molecular sponges for a microRNA through their miRNA binding sites (also ...
PAR-CLIP, another method for identifying the binding sites of cellular RNA-binding proteins (RBPs). RIP-Chip, same goal and ... ChiRP-Seq to measure RNA-bound DNA and proteins. ChIP-exo uses exonuclease treatment to achieve up to single base-pair ... Tag densities at the binding sites are a good indicator of protein-DNA binding affinity, which makes it easier to quantify and ... Darnell RB (2010) HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley Interdiscip Rev RNA. 1):266-86. ...
Because RNA-binding proteins are frequently components of multi-protein complexes, RNAs bound to non-target proteins may be co- ... is a biochemical method used for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ... RNA-protein interactions relied on either the affinity purification of RNA-binding proteins or the immunoprecipitation of RNA- ... CLIP-based techniques can be used to map RNA binding protein binding sites or RNA modification sites of interest on a genome- ...
... the proteins involved in mRNA transport (RNA-binding proteins, RBPs). DLM1 encodes a Z-DNA binding protein. Z-DNA formation is ... DLM1 then binds to cytosolic Viral DNA using two Z-DNA-binding domains (Zα and Zβ) at its N-terminus along with a DNA binding ... Z-DNA-binding protein 1, also known as DNA-dependent activator of IFN-regulatory factors (DAI) and DLM-1, is a protein that in ... ZBP1 is also an abbreviation for chicken or rat β-actin zipcode-binding protein 1, a homolog of the human insulin-like growth ...
In the present report we show the involvement of the RNA-binding proteins (RBPs) embryonic lethal abnormal vision (ELAV) in the ... Our study demonstrates a specific binding between HO-1 messenger RNA (mRNA) and ELAV proteins, accompanied by an increased ... Our study demonstrates a specific binding between HO-1 mRNA and ELAV proteins in a human neuroblastoma cell line treated with ... expression of HO-1 at protein level, in a human neuroblastoma cell line treated with hemin. Clarifying the induction of HO-1 ...
Hence, they fully depend on the maternal mRNAs and proteins stored during oocyte maturation to drive the onset of development. ... Translation regulation often occurs by binding of RNA binding proteins (RBPs) to the 3′UTR of the mRNA [43]. Analysis of the 3′ ... For this reason, RNAs are always bound to proteins in complexes called ribonucleoproteins (RNPs) within the cell. RNPs, in turn ... which is pre-localized at the anterior pole of the oocyte through interaction with sequence-specific RNA-binding proteins (RBPs ...
RNA-binding proteins (RBPs) and microRNAs (miRNAs). Here, we review the RBPs and miRNAs that modulate mRNA turnover and ... and cytoplasmic polyadenylation-element-binding proteins (CPEBs), selectively bind to numerous hypoxia-regulated transcripts ... RNA-binding proteins (RBPs) and microRNAs (miRNAs). Here, we review the RBPs and miRNAs that modulate mRNA turnover and ... iron-response element binding proteins (IRPs), and cytoplasmic polyadenylation-element-binding proteins (CPEBs), selectively ...
... we look at the role of a class of proteins that bind to RNA molecules (RNA-binding proteins, or RBPs) in the regulation of RNA ... we look at the role of a class of proteins that bind to RNA molecules (RNA-binding proteins, or RBPs) in the regulation of RNA ... These sequence motifs act by binding to sequence-specific RNA-binding proteins (RBPs), which in turn modulate the interaction ... 1. RNA-binding proteins whose inactivation causes changes in RNA levels. Numbers of RNAs whose expression is increased (bars on ...
RNA-binding proteins (RBPs) are key regulators of gene expression. Notably, germ cells deploy many distinct RBPs to guide their ... We propose that one major barrier to RNA interference (RNAi)-based therapy is that the siRNA must form a bound complex with a " ... RNA-binding proteins contribute to this polarization by generating diverse subcellular transcriptomes. The RNA-binding protein ... This study reports the RNA interactome for hnRNP R. The main interacting RNA of hnRNP R was the noncoding RNA 7SK. Depletion of ...
Background Circular RNAs (circRNAs) have recently been found to be expressed in human brain tissue, and many lines ofevidence ... Some circRNAs can also regulate miRNAs through RNA-binding proteins (RBPs) and affect cellular function, indicating another ... CircRNAs from the muscle blind (mbl) and FOXO3 genes were reported to bind,sequester andtransport RBPs [34]. The researchers ... RNA binding and protein binding. These significantly enriched GO terms are closely associated with CNS development, suggesting ...
RNA-binding proteins (often abbreviated as RBPs) are proteins that bind to the double or single stranded RNA in cells and ... RNA-binding protein database starBase platform: a platform for decoding binding sites of RNA binding proteins (RBPs) from large ... identification of RNA-binding proteins has extended the number of RNA-binding proteins significantly RNA-binding protein Sam68 ... intricacy of protein-RNA recognition of RRM as it entails RNA-RNA and protein-protein interactions in addition to protein-RNA ...
... noncoding RNA) only. They were subsequently named as circRNAs (circular RNAs) due to the... ... A new type of RNAs was identified from genes traditionally thought to express messenger or linear ncRNA ( ... As in the Intron-Driven Circulation Path, some RBPs (RNA binding proteins) can bind to specific targets in introns and bring ... Controlling the editor: the many roles of RNA-binding proteins in regulating A-to-I RNA editing. Adv Exp Med Biol. 2016;907:189 ...
RNA-binding proteins (RBPs) are essential in RNA metabolism, from synthesis to degradation. RBPs coordinate elaborate networks ... Because FXR1 regulates ECT2 expression without binding to the ECT2 protein, we tested whether FXR1 binds to ECT2 mRNA. We ... Further profiling of FXR1 RNA protein complexes to identify potential binding proteins or mRNAs in cancer versus normal cells ... of RNA-protein and protein-protein interactions that link RNA metabolism to signal transduction pathways (11). Aberrant ...
For each protein that reproducibly bound measurable quantities of bulk RNA (90 % of the panel), we detect enrichment for ... to survey the RNA associated with a panel of 24 chromatin regulators and traditional RNA binding proteins. ... For each protein, we find that the enriched sets of RNAs share distinct biochemical, functional, and chromatin properties. Thus ... However, it is unknown if these observations are specialized instances for a few key RNAs and chromatin factors in specific ...
Several in vitro studies have demonstrated that the Hu proteins bind to RNA. HuB was found to bind to AU-rich RNA sequences in ... Two distinct families of mammalian neuron-specific RNA binding proteins (n-RBPs) have been identified as target antigens in the ... 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. ...
... analysis of the mRNAs associated with a TRIM-NHL protein and the first identification of an RNA motif bound by this protein ... BRAT was thought to be recruited to mRNAs indirectly through interaction with the RNA-binding protein Pumilio (PUM). However, ... BRAT binds mRNAs that encode proteins associated with a variety of functions, many of which are distinct from those implemented ... it has recently been demonstrated that BRAT directly binds to RNA. The precise sequence recognized by BRAT, the extent of BRAT- ...
RNA-binding proteins (RBPs) control the fate of nearly every transcript in a cell. However, no existing approach for studying ... The impact of Vts1 on transcript abundance was largely independent of where it bound within an mRNA, challenging prevailing ... Comprehensive and quantitative mapping of RNA-protein interactions across a transcribed eukaryotic genome PROCEEDINGS OF THE ... Instead, they are highly enriched in nucleic acid binding proteins with large intrinsically disordered domains that have been ...
Most of these processes are inevitably achieved either directly or indirectly by RNA-binding proteins (RBPs) (Keene, 2001; ... AtBRNs bind to the 3′ UTR of SOC1 mRNA in vivo. AtBRNs bind specifically to SOC1 3′ UTR in vivo. Green fluorescent protein (GFP ... RNA-protein binding reactions were carried out in 5× binding buffer (10 mg BSA, 250 mM KCl, 10 mM MgCl2, 5 mM EDTA, 5 mM DTT, 1 ... Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant ...
d) CircRNA biogenesis, mediated by trans-acting factors, such as RNA-binding proteins (RBPs) (e.g., QKI, MBL/MBNL1) that bind ... b) CircRNAs may act as protein sponges, by binding RNA-binding proteins (RBPs). (c) Some circRNAs may regulate protein ... This phenomenon results in the formation of EIciRNAs [21]. The important role of RNA-binding proteins (RBPs) has been ... The starBase v2.0 database has been developed to systematically identify RNA-RNA and protein-RNA interaction networks from ...
RNA-binding proteins (RBPs) and microRNAs (miRNAs). Here, we review the RBPs and miRNAs that modulate mRNA turnover and ... suggesting that both miR-196b and HuD bind to the same RNA element. We present data suggesting that the RNA-binding protein HuD ... The RNA-binding protein TIAR is an mRNA-binding protein that acts as a translational repressor, particularly important under ... Novel RNA-binding Protein P311 Binds Eukaryotic Translation Initiation Factor 3 Subunit b (eIF3b) to Promote Translation of ...
Mapped regions of untranslated, polyadenylated transcriptome bound by RNA-binding proteins (RBPs). ... isoforms in yeast were measured by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing ... Simultaneous mapping of RNA ends by sequencing (SMORE-seq) to identify the strongest transcription start sites and ... Genome binding/occupancy profiling of single nucleosomes and linkers by high throughput sequencing. ...
One mechanism by which immune cells control mRNA levels is through RNA-binding proteins (RBPs). These proteins bind mRNA ... These RNAs prevent DNA-protein interaction by binding DNA-binding motifs or preventing protein-protein interactions (reviewed ... long noncoding RNA. miRNA. microRNA. mTOR. mammalian target of rapamycin. RBP. RNA-binding protein. RISC. RNA-induced silencing ... and its activity is controlled by the eIF4E-binding proteins. (7) Poly(A)-binding proteins cause circularization of mRNAs and ...
lncRNAs, long noncoding RNAs; RBPs, RNA-binding proteins; MTs, metallothioneins.. Finally, whereas oxidative stress is a well- ... TIA1 binds to U-rich sequences close to 5′ SS, enhancing the recruitment of U1 snRNP by the protein-protein interaction between ... Analysis of turnover and translation regulatory RNA-binding protein expression through binding to cognate mRNAs. Mol Cell Biol ... and/or RNA-binding proteins and RNAs. This agrees with recent findings (which our observations confirm) showing that there is a ...
SDS/PAGE showed many bound proteins under all three conditions, but target RNA binding was clearly different from control RNA ... splicing factors/RNA helicases, translation-related proteins, RNA degradation-related proteins, and other RBPs known to be ... RNA affinity mass spectrometry. RBP. RNA binding protein. RIP. RNA co-immunoprecipitation. RRHO. rank-rank hypergeometric ... 2010) Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure. RNA 16, 1096-1107. ...
Many of these protein molecules bind the RNA directly (RBPs). Fusing these RBPs to fluorescent proteins (FPs) is a widely used ... A common drawback of these phage-loop/loop binding coat protein systems is that they rely on transgenic modification of the RNA ... Then how do you follow RNA live? RNA never exists naked within cells - it is always in complex with a dynamic set of protein ... nuclease-resistant oligos can also be targeted against RNA secondary structures and/or protein binding interfaces of interest. ...
RBPs were incubated with a 75-fold excess of an RNA pool and the binding preferences of the RBP elucidated by analysing bound ... Comprehensive analysis of RNA-binding protein effects on AS. We annotated RNA binding proteins (RBPs) in our reference ... Based on homology searches and presence of RNA binding domains, we identified over 300 putative RNA binding proteins in ... AS is chiefly regulated by RNA binding proteins (RBPs), which are themselves often differentially expressed in a cell type- ...
Here, the authors present an integrated mass spectrometry-based approach that allows them to define the Drosophila RNA-protein ... Comprehensive characterisation of RNA-protein interactions requires different levels of resolution. ... This approach was used to identify around 1800 mammalian direct RNA-binding proteins (RBPs), including hundreds of novel RBPs, ... The protein-centric angle relies on isolating proteins and sequencing the RNAs bound to them4,5,6,7. On the other hand, the RNA ...
Its beneficial when RNA and RNA-binding proteins (RBPs) form dynamic liquid assemblies required for many cell functions. Its ... they predict that changes in RNA levels or the ability of proteins to bind RNA are frequent causes of age-related protein- ... They show that not only proteins and protein modifications play a role in RNA-binding protein biology and pathology, but ... RNA buffers the phase separation behavior of prion-like RNA binding proteins. Science. 2018 Apr 12;. PubMed. ...
The importance of microRNAs and RNA binding proteins (RBPs) is now beginning to be better appreciated. We study the elav ( ... The elav family of RBPs binds to the AU-rich elements (AREs) found in the 3\#8217; untranslated regions (UTRs) of many early- ... Abstract #3808: RNA immunoprecipitations (RIP-on-Chip) identify unique subsets of genes in ER+ and ER- breast cancer. Ulus ... We have developed methods which enable us to identify en masse, in vivo targets of RBPs such as HuR from cell lines and now for ...
  • CircRNA was found extensive in eukaryotic cells by deep sequencing technologies, and a large number of researches suggested that it possesses complicated functions such as competing with linear RNAs in the splicing, working as endogenous RNAs to sponge miRNAs, regulating transcription and so on [ 3 , 4 ], and it seems that other important but underlying functions will be revealed as soon as possible. (springer.com)
  • They may be also translated in a cap-independent manner in vivo , to generate specific proteins. (hindawi.com)
  • P311, a conserved, 8-kDa, intracellular protein expressed in brain, smooth muscle, regenerating tissues, and malignant glioblastomas, represents the first-documented pan-stimulator of TGF-?1-3 translation in vitro and in vivo. (jove.com)
  • This method critically relies on in vivo UV crosslinking and allows for the isolation and identification of plant mRNA-binding proteins from a physiological environment. (jove.com)
  • This depends on the RNA helicase DDX1 that is also required for CSR in vivo. (babraham.ac.uk)
  • RBPs have crucial roles in various cellular processes such as: cellular function, transport and localization. (wikipedia.org)
  • To investigate their cellular dynamics, we developed a quantitative assay, which detects differences in nucleocytoplasmic shuttling among seven canonical SR protein family members. (rupress.org)
  • Cellular localization assays suggested that both proteins are mainly distributed in the cytoplasm of promastigotes growing at 26 °C, but they accumulate in foci around the nucleus when the parasites are under heat-shock conditions. (biomedcentral.com)
  • However, in these conditions, the cellular content of both proteins remained unaltered. (biomedcentral.com)
  • We use a number of cellular and molecular biology tools together with mouse genetics, cellular model systems and in vitro biochemical assays, to investigate the function of RBPs in B cells. (babraham.ac.uk)
  • We report cellular, genetic, biochemical, substrate selectivity, and crystallographic studies providing evidence that an additional endoribonuclease, MBL domain containing protein 1 (MBLAC1), is selective for 3' processing of RD histone pre-mRNA during the S-phase of the cell cycle. (babraham.ac.uk)
  • Crucially, with the advent of methods that allow measurement of protein translation rates on a global scale, it has become apparent that translational control seems to be the defining step in determining the steady-state levels of most cellular proteins. (rsc.org)
  • Indeed, BRAT-mediated repression of hb has served as a model for understanding the mechanisms by which TRIM-NHL proteins function as post-transcriptional regulators. (biomedcentral.com)
  • Microarray technologies assessing global mRNA levels in cells are only partially valid because posttranscriptional mechanisms dramatically affect protein levels in the proteome. (jimmunol.org)
  • Recent studies showed that ∼30% of protein levels actually correspond to mRNA levels at steady-state, suggesting that mechanisms solely regulating gene transcription or mRNA stability do not necessarily affect protein levels in cells and that changes in mRNA expression profiles frequently do not correspond to those seen in the cell's proteome ( 5 , 6 ). (jimmunol.org)
  • Exploiting RNA as a programmable antibiotic to treat bacterial infections and dysbiosis requires that we comprehensively understand the major RNA -based pathways and mechanisms in these species. (helmholtz-hzi.de)
  • While transcription controls only the rate of RNA production, numerous and diverse mechanisms regulate the processing, stability and translation of RNAs at the post-transcriptional level. (upenn.edu)
  • Selective activation or inhibition of a particular protein function can help elucidate crucial molecular mechanisms and enables important advances in cell biology. (ku.edu)
  • 3) Construct predictive models using machine learning and implement "iDiscover", the intelligent web interface, which will lead researchers in discovering regulatory mechanisms of individual RBPs. (uni-lj.si)
  • 4) Integrate data from HTS methods for understanding molecular mechanisms of two proteins, which are associated with neurodegenerative diseases: TD-43 and FUS. (uni-lj.si)
  • Previous findings on the RNA helicase DDX1 have shown that RBPs can directly regulate RNA function and be part of antibody gene recombination mechanisms (Ribeiro de Almeida et al, 2018). (babraham.ac.uk)
  • In embryos from pum , brat , or nos mutant mothers, HB protein is ectopically expressed in the posterior of the embryo, leading to a loss of abdominal cell fates and embryonic lethality [ 3 - 8 ]. (biomedcentral.com)
  • We study the elav (embryonic lethal abnormal vision) family of RBPs, which are paraneoplastic antigens, over-expressed in a variety of malignancies, including breast cancer. (aacrjournals.org)
  • Experiments on early mouse embryos and using inducible Xist transgenes in mouse embryonic stem cells (mESCs) revealed that Polycomb recruitment in X inactivation is strictly dependent on ongoing Xist RNA expression [ 1 , 2 ]. (royalsocietypublishing.org)
  • We demonstrate that MAPs are competing for microtubule binding sites in the spindle suggesting a simple model how spindle composition and morphology could adapt to the drastically changing cell sized in early embryonic development. (ushupo.org)
  • Dr. Martha Cyert directs a research lab that studies Ca2+-dependent signal transduction, focusing on calcineurin, the highly conserved Ca2+/calmodulin-regulated protein phosphatase that plays critical roles in muscle, immune and neural cells. (stanford.edu)
  • We demonstrate its application to a number of different studies revealing some surprising roles as RBPs for a variety of different metabolic proteins. (ushupo.org)
  • RBPs are important to regulate RNA fate and function, and our understanding of their roles in B cells is only emerging. (babraham.ac.uk)
  • Our results demonstrate that P311 is a novel RNA-binding protein that by interacting with TGF-?s 5'UTRs and eIF3b stimulates the translation of TGF-?1, 2 and 3. (jove.com)
  • As a class of non-coding RNAs, circRNAs are characterized by covalently closed continuous loop. (springer.com)
  • Their unique circular structure makes circRNAs more stable than linear RNAs. (hindawi.com)
  • In the last decade, next-generation sequencing techniques, especially RNA-seq, have revealed great abundance and also dysregulation of many circRNAs in various diseases, suggesting their involvement in disease development and progression. (hindawi.com)
  • In the last decade, RNA-seq and other next-generation sequencing techniques have enabled a significant breakthrough in circRNA discovery, leading to the identification and characterization of a large number of circRNAs in humans and other eukaryotes [ 9 , 10 ]. (hindawi.com)
  • We performed circRNAs microarray using exosomal RNAs from HCT116-R and HCT116-P cells. (nature.com)
  • Many of these circRNAs are stable and contain exons, but are not translated into proteins. (springer.com)
  • Axotomy increases axonal transport of hnRNPs H1, F, and K, depletion of these hnRNPs decreases axon growth and reduces axonal mRNA levels and axonal protein synthesis. (mcponline.org)
  • Through collaborative and multidisciplinary efforts, we find that the switchable proteins built via the chemical rescue of structure are frequently controlled indirectly by modulating protein stability, rather than discrete conformational changes. (ku.edu)
  • Since energetic evaluation of protein stability is far more tractable than designing and/or predicting allosteric conformational changes, this finding demonstrates how chemical rescue of structure can be applied to other systems for building a variety of new protein switches. (ku.edu)
  • However, mRNA levels in cells frequently do not correlate with the levels of proteins in the proteome ( 1 - 4 ), emphasizing the existence of an "expression gap" between the transcriptome and mRNA translation (translatome). (jimmunol.org)
  • One mechanism by which immune cells control mRNA levels is through RNA-binding proteins (RBPs). (jimmunol.org)
  • Results further indicate that in L. mexicana parasites, mRNA levels are not a strong predictor of whole cell expression or RNA binding potential of encoded proteins. (mcponline.org)
  • As absorption and emission spectra of TO are sufficiently different from that of EGFP, this enables high sensitivity and specificity RNA-protein co-localization analysis, even with super-resolution, complementing classical biochemistry based discovery of the RNA interactome. (leica-microsystems.com)
  • Finally, we applied a recently developed approach to isolate and sequence AGO-bound microRNA precursors (pre-miRNAs). (upenn.edu)
  • Disruption of P311-eIF3b binding inhibited translation of TGF-?1, 2 and 3, as indicated by luciferase reporter assays, polysome fractionation studies, and western blot analysis. (jove.com)
  • This work was aimed to do a structural and biochemical characterization of two Leishmania braziliensis proteins, which were previously found in pull-down assays using an HSP70 RNA as bait. (biomedcentral.com)
  • Calcineurin, the conserved Ca2+/calmodulin-dependent protein phosphatase and target of immunosuppressants, FK506 and Cyclosporin A, is ubiquitously expressed, and critically regulates Ca2+-dependent processes in the immune system, heart, and brain. (stanford.edu)
  • Indeed, together with TIA1-like/TIA1-related protein (TIAL1/TIAR) ( 21 , 22 ), TIA1 has direct regulatory control of over 10 to 20% of the human transcriptome ( 19 , 20 ). (asm.org)
  • ChEC-seq to map the genome-wide binding of the SAGA coactivator complex in budding yeast. (yeastgenome.org)
  • To gain insight into the nature and extent of this mRNA-dependent crosstalk in human cells, we aim to determine the target sets of several rRBPs on a genome-wide level and compare them with those of the Argonaute proteins (huAGO1-4). (openwetware.org)
  • The role of transforming growth factorβ (TGF-β)-induced tumor progression in advanced malignancy is well established, but the involvement of long non-coding RNAs (lncRNAs) in TGF-β signaling remains unclear. (biomedcentral.com)
  • This leads to the formation of extended, polyadenylated lncRNAs that are both chromatin restricted and form increased levels of RNA:DNA hybrid (R-loops) that are associated with DNA damage. (babraham.ac.uk)