The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
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.
The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.
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)
Ribonucleic acid that makes up the genetic material of viruses.
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 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.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
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).
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.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
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 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)
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
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.
Viruses whose genetic material is RNA.
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).
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.
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.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
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.
The processes of RNA tertiary structure formation.
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.
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.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
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 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.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
A family of proteins that promote unwinding of RNA during splicing and translation.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
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.
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.
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.
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.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
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 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).
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 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.
Established cell cultures that have the potential to propagate indefinitely.
Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
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.
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.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
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 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 present in neoplastic tissue.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.
Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.
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.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
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.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
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.
Nucleic acid sequences involved in regulating the expression of genes.
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.
Complexes of RNA-binding proteins with ribonucleic acids (RNA).
The parts of a macromolecule that directly participate in its specific combination with another molecule.
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.
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.
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.
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.
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)
RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.
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.
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 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.
Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.
An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.
Small, linear single-stranded RNA molecules functionally acting as molecular parasites of certain RNA plant viruses. Satellite RNAs exhibit four characteristic traits: (1) they require helper viruses to replicate; (2) they are unnecessary for the replication of helper viruses; (3) they are encapsidated in the coat protein of the helper virus; (4) they have no extensive sequence homology to the helper virus. Thus they differ from SATELLITE VIRUSES which encode their own coat protein, and from the genomic RNA; (=RNA, VIRAL); of satellite viruses. (From Maramorosch, Viroids and Satellites, 1991, p143)
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.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A codon that directs initiation of protein translation (TRANSLATION, GENETIC) by stimulating the binding of initiator tRNA (RNA, TRANSFER, MET). In prokaryotes, the codons AUG or GUG can act as initiators while in eukaryotes, AUG is the only initiator codon.
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.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
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.
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.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
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.
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).
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.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. The enzyme functions in the nucleolar structure and transcribes DNA into RNA. It has different requirements for cations and salts than RNA polymerase II and III and is not inhibited by alpha-amanitin. EC 2.7.7.6.
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.
Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Deletion of sequences of nucleic acids from the genetic material of an individual.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
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.
Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.
The steps that generate the 3' ends of mature RNA molecules. For most mRNAs (RNA, MESSENGER), 3' end processing referred to as POLYADENYLATION includes the addition of POLY A.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
The relationships of groups of organisms as reflected by their genetic makeup.
Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.
A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.
Any method used for determining the location of and relative distances between genes on a chromosome.
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)
Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.
Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
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.
Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.
The small RNAs which provide spliced leader sequences, SL1, SL2, SL3, SL4 and SL5 (short sequences which are joined to the 5' ends of pre-mRNAs by TRANS-SPLICING). They are found primarily in primitive eukaryotes (protozoans and nematodes).
A genus of FLAVIVIRIDAE causing parenterally-transmitted HEPATITIS C which is associated with transfusions and drug abuse. Hepatitis C virus is the type species.
A process of GENETIC TRANSLATION whereby the formation of a peptide chain is started. It includes assembly of the RIBOSOME components, the MESSENGER RNA coding for the polypeptide to be made, INITIATOR TRNA, and PEPTIDE INITIATION FACTORS; and placement of the first amino acid in the peptide chain. The details and components of this process are unique for prokaryotic protein biosynthesis and eukaryotic protein biosynthesis.
Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).
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.
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)
Viruses parasitic on plants higher than bacteria.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
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.
A superfamily of proteins containing the globin fold which is composed of 6-8 alpha helices arranged in a characterstic HEME enclosing structure.
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.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.
A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
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 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.
A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.
Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.
An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.
A family of small RNA viruses comprising some important pathogens of humans and animals. Transmission usually occurs mechanically. There are nine genera: APHTHOVIRUS; CARDIOVIRUS; ENTEROVIRUS; ERBOVIRUS; HEPATOVIRUS; KOBUVIRUS; PARECHOVIRUS; RHINOVIRUS; and TESCHOVIRUS.
Deoxyribonucleic acid that makes up the genetic material of viruses.
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.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
A family of RNA plant viruses infecting dicotyledons. Transmission is mainly by mechanical inoculation and through propagative plant material. All species elicit formation of multivesicular inclusion bodies. There are at least eight genera: Aureusvirus, Avenavirus, CARMOVIRUS, Dianthovirus, Machlomovirus, Necrovirus, Panicovirus, and TOMBUSVIRUS.
Neuromuscular disorder characterized by PROGRESSIVE MUSCULAR ATROPHY; MYOTONIA, and various multisystem atrophies. Mild INTELLECTUAL DISABILITY may also occur. Abnormal TRINUCLEOTIDE REPEAT EXPANSION in the 3' UNTRANSLATED REGIONS of DMPK PROTEIN gene is associated with Myotonic Dystrophy 1. DNA REPEAT EXPANSION of zinc finger protein-9 gene intron is associated with Myotonic Dystrophy 2.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
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.
A genus in the family TOMBUSVIRIDAE mostly found in temperate regions. Some species infecting legumes (FABACEAE) are reported from tropical areas. Most viruses are soil-borne, but some are transmitted by the fungus Olpidium radicale and others by beetles. Carnation mottle virus is the type species.
The rate dynamics in chemical or physical systems.
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
The functional hereditary units of VIRUSES.
A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
A cell line derived from cultured tumor cells.
A reaction that severs one of the sugar-phosphate linkages of the phosphodiester backbone of RNA. It is catalyzed enzymatically, chemically, or by radiation. Cleavage may be exonucleolytic, or endonucleolytic.
Short RNA, about 200 base pairs in length or shorter, that does not code for protein.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Proteins encoded by a VIRAL GENOME that are produced in the organisms they infect, but not packaged into the VIRUS PARTICLES. Some of these proteins may play roles within the infected cell during VIRUS REPLICATION or act in regulation of virus replication or VIRUS ASSEMBLY.
The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
Interruption or suppression of the expression of a gene at transcriptional or translational levels.
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.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
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.
Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.
RNA sequences composed of ADENINE NUCLEOTIDES and URACIL NUCLEOTIDES, that are located in the 3'UNTRANSLATED REGIONS of MESSENGER RNA molecules that are rapidly degraded. They are also known as AREs.
A species of ENTEROVIRUS which is the causal agent of POLIOMYELITIS in humans. Three serotypes (strains) exist. Transmission is by the fecal-oral route, pharyngeal secretions, or mechanical vector (flies). Vaccines with both inactivated and live attenuated virus have proven effective in immunizing against the infection.
The sum of the weight of all the atoms in a molecule.
Proteins prepared by recombinant DNA technology.
Viruses which produce a mottled appearance of the leaves of plants.
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 species of CORONAVIRUS infecting neonatal calves, presenting as acute diarrhea, and frequently leading to death.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Plants or plant parts which are harmful to man or other animals.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Biochemical identification of mutational changes in a nucleotide 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.
A method (first developed by E.M. Southern) for detection of DNA 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.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
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.
Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
The outer protein protective shell of a virus, which protects the viral nucleic acid.
Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.
Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.
An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 3.1.27.3.
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.
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.
Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.
Genotypic differences observed among individuals in a population.
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.
Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.
Proteins found in any species of bacterium.
Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.
Any codon that signals the termination of genetic translation (TRANSLATION, GENETIC). PEPTIDE TERMINATION FACTORS bind to the stop codon and trigger the hydrolysis of the aminoacyl bond connecting the completed polypeptide to the tRNA. Terminator codons do not specify amino acids.
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 genus of plant viruses that infects both monocotyledonous and dicotyledonous plants. Its organisms are persistently transmitted by aphids, and weeds may provide reservoirs of infection.
A species of CERCOPITHECUS containing three subspecies: C. tantalus, C. pygerythrus, and C. sabeus. They are found in the forests and savannah of Africa. The African green monkey (C. pygerythrus) is the natural host of SIMIAN IMMUNODEFICIENCY VIRUS and is used in AIDS research.
Synthetic transcripts of a specific DNA molecule or fragment, made by an in vitro transcription system. This cRNA can be labeled with radioactive uracil and then used as a probe. (King & Stansfield, A Dictionary of Genetics, 4th ed)

X inactive-specific transcript (Xist) expression and X chromosome inactivation in the preattachment bovine embryo. (1/2581)

Expression of the X inactive-specific transcript (Xist) is thought to be essential for the initiation of X chromosome inactivation and dosage compensation during female embryo development. In the present study, we analyzed the patterns of Xist transcription and the onset of X chromosome inactivation in bovine preattachment embryos. Reverse transcription-polymerase chain reaction (RT-PCR) revealed the presence of Xist transcripts in all adult female somatic tissues evaluated. In contrast, among the male tissues examined, Xist expression was detected only in testis. No evidence for Xist transcription was observed after a single round of RT-PCR from pools of in vitro-derived embryos at the 2- to 4-cell stage. Xist transcripts were detected as a faint amplicon at the 8-cell stage initially, and consistently thereafter in all stages examined up to and including the expanded blastocyst stage. Xist transcripts, however, were subsequently detected from the 2-cell stage onward after nested RT-PCR. Preferential [3H]thymidine labeling indicative of late replication of one of the X chromosomes was noted in female embryos of different developmental ages as follows: 2 of 7 (28.5%) early blastocysts, 6 of 13 (46.1%) blastocysts, 8 of 11 (72.1%) expanded blastocysts, and 14 of 17 (77.7%) hatched blastocysts. These results suggest that Xist expression precedes the onset of late replication in the bovine embryo, in a pattern compatible with a possible role of bovine Xist in the initiation of X chromosome inactivation.  (+info)

Parental allele-specific chromatin configuration in a boundary-imprinting-control element upstream of the mouse H19 gene. (2/2581)

The mouse H19 gene is expressed from the maternal chromosome exclusively. A 2-kb region at 2 to 4 kb upstream of H19 is paternally methylated throughout development, and these sequences are necessary for the imprinted expression of both H19 and the 5'-neighboring Igf2 gene. In particular, on the maternal chromosome this element appears to insulate the Igf2 gene from enhancers located downstream of H19. We analyzed the chromatin organization of this element by assaying its sensitivity to nucleases in nuclei. Six DNase I hypersensitive sites (HS sites) were detected on the unmethylated maternal chromosome exclusively, the two most prominent of which mapped 2.25 and 2.75 kb 5' to the H19 transcription initiation site. Five of the maternal HS sites were present in expressing and nonexpressing tissues and in embryonic stem (ES) cells. They seem, therefore, to reflect the maternal origin of the chromosome rather than the expression of H19. A sixth maternal HS site, at 3.45 kb upstream of H19, was detected in ES cells only. The nucleosomal organization of this element was analyzed in tissues and ES cells by micrococcal nuclease digestion. Specifically on the maternal chromosome, an unusual and strong banding pattern was obtained, suggestive of a nonnucleosomal organization. From our studies, it appears that the unusual chromatin organization with the presence of HS sites (maternal chromosome) and DNA methylation (paternal chromosome) in this element are mutually exclusive and reflect alternate epigenetic states. In addition, our data suggest that nonhistone proteins are associated with the maternal chromosome and that these might be involved in its boundary function.  (+info)

Xist yeast artificial chromosome transgenes function as X-inactivation centers only in multicopy arrays and not as single copies. (3/2581)

X-chromosome inactivation in female mammals is controlled by the X-inactivation center (Xic). This locus is required for inactivation in cis and is thought to be involved in the counting process which ensures that only a single X chromosome remains active per diploid cell. The Xist gene maps to the Xic region and has been shown to be essential for inactivation in cis. Transgenesis represents a stringent test for defining the minimal region that can carry out the functions attributed to the Xic. Although YAC and cosmid Xist-containing transgenes have previously been reported to be capable of cis inactivation and counting, the transgenes were all present as multicopy arrays and it was unclear to what extent individual copies are functional. Using two different yeast artificial chromosomes (YACs), we have found that single-copy transgenes, unlike multicopy arrays, can induce neither inactivation in cis nor counting. These results demonstrate that despite their large size and the presence of Xist, the YACs that we have tested lack sequences critical for autonomous function with respect to X inactivation.  (+info)

Genetic analysis of the mouse X inactivation center defines an 80-kb multifunction domain. (4/2581)

Dosage compensation in mammals occurs by X inactivation, a silencing mechanism regulated in cis by the X inactivation center (Xic). In response to developmental cues, the Xic orchestrates events of X inactivation, including chromosome counting and choice, initiation, spread, and establishment of silencing. It remains unclear what elements make up the Xic. We previously showed that the Xic is contained within a 450-kb sequence that includes Xist, an RNA-encoding gene required for X inactivation. To characterize the Xic further, we performed deletional analysis across the 450-kb region by yeast-artificial-chromosome fragmentation and phage P1 cloning. We tested Xic deletions for cis inactivation potential by using a transgene (Tg)-based approach and found that an 80-kb subregion also enacted somatic X inactivation on autosomes. Xist RNA coated the autosome but skipped the Xic Tg, raising the possibility that X chromosome domains escape inactivation by excluding Xist RNA binding. The autosomes became late-replicating and hypoacetylated on histone H4. A deletion of the Xist 5' sequence resulted in the loss of somatic X inactivation without abolishing Xist expression in undifferentiated cells. Thus, Xist expression in undifferentiated cells can be separated genetically from somatic silencing. Analysis of multiple Xic constructs and insertion sites indicated that long-range Xic effects can be generalized to different autosomes, thereby supporting the feasibility of a Tg-based approach for studying X inactivation.  (+info)

A developmental switch in H4 acetylation upstream of Xist plays a role in X chromosome inactivation. (5/2581)

We have investigated the role of histone acetylation in X chromosome inactivation, focusing on its possible involvement in the regulation of Xist, an essential gene expressed only from the inactive X (Xi). We have identified a region of H4 hyperacetylation extending up to 120 kb upstream from the Xist somatic promoter P1. This domain includes the promoter P0, which gives rise to the unstable Xist transcript in undifferentiated cells. The hyperacetylated domain was not seen in male cells or in female XT67E1 cells, a mutant cell line heterozygous for a partially deleted Xist allele and in which an increased number of cells fail to undergo X inactivation. The hyperacetylation upstream of Xist was lost by day 7 of differentiation, when X inactivation was essentially complete. Wild-type cells differentiated in the presence of the histone deacetylase inhibitor Trichostatin A were prevented from forming a normally inactivated X, as judged by the frequency of underacetylated X chromosomes detected by immunofluorescence microscopy. Mutant XT67E1 cells, lacking hyperacetylation upstream of Xist, were less affected. We propose that (i) hyperacetylation of chromatin upstream of Xist facilitates the promoter switch that leads to stabilization of the Xist transcript and (ii) that the subsequent deacetylation of this region is essential for the further progression of X inactivation.  (+info)

Both transcriptional and posttranscriptional mechanisms regulate human telomerase template RNA levels. (6/2581)

The human telomerase RNA component (hTR) is present in normal somatic cells at lower levels than in cancer-derived cell lines. To understand the mechanisms regulating hTR levels in different cell types, we have compared the steady-state hTR levels in three groups of cells: (i) normal telomerase-negative human diploid cells; (ii) normal cells transfected with the human telomerase catalytic subunit, hTERT; and (iii) cells immortalized in vitro and cancer cells expressing their own endogenous hTERT. To account for the differences in steady-state hTR levels observed in these cell types, we compared the transcription rate and half-life of hTR in a subset of these cells. The half-life of hTR in telomerase-negative cells is about 5 days and is increased 1.6-fold in the presence of hTERT. The transcription rate of hTR is essentially unchanged in cells expressing exogenous hTERT, and the increased steady-state hTR level appears to be due to the increased half-life. However, the transcription rate of hTR is greatly increased in cells expressing endogenous hTERT, suggesting some overlap in transcriptional regulatory control. We conclude that the higher hTR level in cells expressing an endogenous telomerase can be a result of both increased transcription and a longer half-life and that the longer half-life might be partially a result of protection or stabilization by the telomerase catalytic subunit. The 4-week half-life of hTR in H1299 tumor cells is the longest half-life yet reported for any RNA.  (+info)

The timing of XIST replication: dominance of the domain. (7/2581)

Contiguous replicons are coordinately replicated and may be organized in temporal-spatial domains with early replication domains containing expressed genes and late ones carrying silent genes. XIST is silent on the active, early replicating X chromosome and expressed from the inactive, late replicating homolog. These circumstances potentially deviate from the aforementioned generalization and make studies of replication timing for XIST of special interest. Although earlier investigations of XIST replication in fibroblasts based on analysis of extracted DNA from cells at different stages of the cell cycle suggested that the silent gene does replicate before the expressed allele, studies using FISH technology produced the opposite results. Because the FISH replication studies could not directly distinguish between the active and inactive X chromosomes in the same cell, we undertook a re-investigation of this question utilizing FISH analysis under conditions that allowed us to make that distinction using cells sorted into different cell cycle stages by flow cytometry. The findings reported here indicate that the silent XIST gene on the active X chromosome does replicate before the expressed allele on the inactive X, supporting the view that the time of a gene's replication is determined by the large, multi-replicon domain in which it is located and not necessarily its expression state.  (+info)

The genotype and epigenotype synergize to diversify the spatial pattern of expression of the imprinted H19 gene. (8/2581)

Little is known of how the genetic background effects the phenomenon of genomic imprinting. The H19 gene belongs to a cluster of imprinted genes on human chromosome 11. Here we show that the alternative splicing of a human H19 transcript is genotype-specific. Moreover, this variant transcript, which lacks exon 4, is either not found at all, is widely expressed or is confined to extra-villous cytotrophoblasts in first trimester placenta, depending on a combination of the genotype and the sex of the transmitting parent.  (+info)

TY - JOUR. T1 - The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4. AU - Ranzani, Valeria. AU - Rossetti, Grazisa. AU - Panzeri, Ilaria. AU - Arrigoni, Alberto. AU - Bonnal, Raoul J P. AU - Curti, Serena. AU - Gruarin, Paola. AU - Provasi, Elena. AU - Sugliano, Elisa. AU - Marconi, Maurizio. AU - De Francesco, Raffaele. AU - Geginat, Jens. AU - Bodega, Beatrice. AU - Abrignani, Sergio. AU - Pagani, Massimiliano. PY - 2015/2/17. Y1 - 2015/2/17. N2 - Long noncoding RNAs are emerging as important regulators of cellular functions, but little is known of their role in the human immune system. Here we investigated long intergenic noncoding RNAs (lincRNAs) in 13 subsets of T lymphocytes and B lymphocytes by next-generation sequencing-based RNA sequencing (RNA-seq analysis) and de novo transcriptome reconstruction. We identified over 500 previously unknown lincRNAs and described lincRNA signatures. Expression of linc-MAF-4, ...
Long intergenic noncoding RNAs (lincRNAs) play important roles in disease, but the vast majority of these transcripts remain uncharacterized. A team led by researchers from Duke University defined a set of 54,944 human lincRNAs by drawing on four publicly available lincRNA datasets, and annotated ~2.5 million single-nucleotide polymorphisms from each of 15 cardiometabolic genome-wide association study datasets into these lincRNAs. They identified hundreds of lincRNAs with at least one trait-associated SNP: 898 SNPs in 343 unique lincRNAs at 5% false discovery rate, and 469 SNPs in 146 unique lincRNAs meeting Bonferroni-corrected P ,0.05. An additional 64 trait-associated lincRNAs were identified using a class-level testing strategy at Bonferroni-corrected P ,0.05. To better understand the genomic context and prioritize trait-associated lincRNAs, the team examined the pattern of linkage disequilibrium between SNPs in the lincRNAs and SNPs that met genome-wide-significance in the region (±500 kb ...
Noncoding RNAs have been extensively described in plant and animal transcriptomes by using high-throughput sequencing technology. Of these non-coding RNAs, a growing number of long intergenic noncoding RNAs (lincRNAs) have been described in multicellular organisms, however the origins and functions of many lincRNAs remain to be explored. In many eukaryotic genomes, transposable elements (TEs) are widely distributed and often account for large fractions of plant and animal genomes yet the contribution of TEs to lincRNAs is largely unknown. By using strand-specific RNA sequencing, researchers from the Shanghai Center for Plant Stress Biology profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified 47, 611 and 398 TE-associated lincRNAs (TE-lincRNAs), respectively. TE-lincRNAs were more often derived from retrotransposons than DNA transposons and as retrotransposon copy number in both rice and maize genomes so did TE-lincRNAs. The researchers validated the ...
Whole transcriptome analyses have revealed a large number of novel transcripts including long and short noncoding RNAs (ncRNAs). Currently, there is great interest in characterizing the functions of the different classes of ncRNAs and their relevance to cellular processes. In particular, nuclear long ncRNAs may be involved in controlling various aspects of biological regulation, such as stress responses. By a combination of bioinformatic and experimental approaches, we identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Some nuclear long ncRNAs were conserved among vertebrates, whereas others were found only among primates. Expression profiling of the nuclear long ncRNAs in human tissues revealed that most were expressed ubiquitously. A subset of the identified nuclear long ncRNAs was induced by the genotoxic agents mitomycin C or doxorubicin, in HeLa Tet-off cells. There were no commonly altered nuclear long ncRNAs between mitomycin C- and doxorubicin-treated cells.
BACKGROUND: Long considered to be the building block of life, it is now apparent that protein is only one of many functional products generated by the eukaryotic genome. Indeed, more of the human genome is transcribed into noncoding sequence than into protein-coding sequence. Nevertheless, whilst we have developed a deep understanding of the relationships between evolutionary constraint and function for protein-coding sequence, little is known about these relationships for non-coding transcribed sequence. This dearth of information is partially attributable to a lack of established non-protein-coding RNA (ncRNA) orthologs among birds and mammals within sequence and expression databases. RESULTS: Here, we performed a multi-disciplinary study of four highly conserved and brain-expressed transcripts selected from a list of mouse long intergenic noncoding RNA (lncRNA) loci that generally show pronounced evolutionary constraint within their putative promoter regions and across exon-intron boundaries. We
Long non-coding RNAs (long ncRNAs, lncRNA) are defined as transcripts longer than 200 nucleotides that are not translated into protein. This somewhat arbitrary limit distinguishes long ncRNAs from small non-coding RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs. However, very recent research has shown that some lncRNAs have been misannotated and do in fact encode proteins. A recent study found only one-fifth of transcription across the human genome is associated with protein-coding genes, indicating at least four times more long non-coding than coding RNA sequences. However, it is large-scale complementary DNA (cDNA) sequencing projects such as FANTOM (Functional Annotation of Mammalian cDNA) that reveal the complexity of this transcription. The FANTOM3 project identified ~35,000 non-coding transcripts from ~10,000 distinct loci that bear many signatures of mRNAs, including 5 capping, ...
Whilst only approximately 1.06% of the human genome appears to encode protein [1, 2] at least four times this amount is transcribed into stable non-protein-coding RNA (ncRNA) transcripts [3-5]. Unfortunately, the biological relevance of the vast majority of this extensive and interleaving network of coding RNAs and ncRNAs remains far from clear. One possibility is that many ncRNAs result simply from transcriptional noise. If so, their sequence and transcription might be expected not to be conserved outside of restricted phyletic lineages. Indeed, the finding that only 14% of the well-defined mouse long intergenic ncRNAs (lncRNAs) identified in the FANTOM projects [6, 7] have a transcribed ortholog in human (based on analyses of known EST and cDNA data sets) [2] argues against their functionality. Similarly, known human intergenic lncRNA loci are generally not conserved in sequence at statistically significant levels in the mouse genome [3, 8, 9], and there is little evidence for conserved ...
Non-protein-coding RNAs (ncRNAs) are increasingly being recognized as having important regulatory roles. Although much recent attention has focused on tiny 22- to 25-nucleotide microRNAs, several functional ncRNAs are orders of magnitude larger in size. Examples of such macro ncRNAs include Xist and Air, which in mouse are 18 and 108 kilobases (Kb), respectively. We surveyed the 102,801 FANTOM3 mouse cDNA clones and found that Air and Xist were present not as single, full-length transcripts but as a cluster of multiple, shorter cDNAs, which were unspliced, had little coding potential, and were most likely primed from internal adenine-rich regions within longer parental transcripts. We therefore conducted a genome-wide search for regional clusters of such cDNAs to find novel macro ncRNA candidates. Sixty-six regions were identified, each of which mapped outside known protein-coding loci and which had a mean length of 92 Kb. We detected several known long ncRNAs within these regions, supporting the basic
So-called long noncoding RNAs (ncRNAs) are transcripts that are larger than small regulatory RNAs, such as microRNAs (miRNAs) and small nucleolar RNAs (snoRNAs), that have traditionally been thought not to encode proteins because they contain only short open reading frames (sORFs). Recent studies, however, have indicated that some sORFs of long ncRNAs are translated. One such translated long ncRNA is that transcribed from the polished rice (pri) locus in the fruit fly Drosophila melanogaster, which encodes four peptides 11 to 32 amino acids in length. Loss-of-function mutations in pri phenocopy loss of shavenbaby (svb), which encodes a transcription factor required for formation of hairs called trichomes on the dorsal epidermis of the fly embryo. Kondo et al. report that, in pri mutants, expression of svb was normal, but expression of genes and reporters activated by Svb was reduced. The svb locus encodes three transcription factor isoforms that share the same DNA binding and transcriptional ...
The majority of the human genome is transcribed into non-protein-coding RNA. Hence, RNA is also the primary product of the cancer genome. We have defined the ncRNA expression landscape of lung, breast and liver cancer providing a comprehensive expression map of over 17000 long ncRNAs and discovering new lncRNAs associated with cancer whose molecular and cellular functions we are currently elucidating exploiting our custom siRNA library targeting 638 tumor-associated lncRNAs. The nuclear lncRNA MALAT1 was one of the first lncRNAs associated with cancer: it is associated with metastasis development in lung cancer. However, its high abundance and nuclear localization have hampered its functional analysis. To uncover its functional importance, we developed a MALAT1 knockout model in human lung tumor cells by genomically integrating RNA destabilizing elements site-specifically into the MALAT1 locus. This approach yielded a 1000-fold silencing of MALAT1 providing a unique loss-of-function model. ...
TY - JOUR. T1 - The non-coding transcripts of hsr-omega gene in Drosophila. T2 - Do they regulate trafficking and availability of nuclear RNA-processing factors?. AU - Lakhotia, S. C.. AU - Ray, Pritha. AU - Rajendra, T. K.. AU - Prasanth, K. V.. PY - 1999/8/25. Y1 - 1999/8/25. N2 - The 93D or hsr-omega (hsrω) is an unusual non-protein-coding gene with multiple transcription products which are dynamically expressed in most cell types of Drosophila melanogaster and this gene, besides being a member of the heat shock gene family, is uniquely induced in polytene cells by a variety of amides. The various aspects of this genes organization, regulation and inducible properties are briefly reviewed. Recent data in our laboratory show that absence of the hsr-omega transcripts because of nullosomy or over-expression of the these transcripts in specific cell types due to mutation in the promoter region of this gene results in specific phenotypes. It is known from several earlier and our recent studies ...
2:30-3:30 PM. Guest Speaker: Chiara Arina (Insitut dAstrophysique de Paris and Université Pierre et Marie Curie (Paris 6)). Talk Title: A WIMP view of particle dark matter: from data analysis to theoretical models. Abstract: The astroparticle experiments have reached unprecedented sensitivities, releasing constantly suggestive hints and stringent constraints that seem to chase each other. Considering as an example the direct dark matter detection data, I will show how uncertainties affect the theoretical interpretation of these bounds/hints. These results serve as guidelines for dark matter model building. I will discuss how inference of the properties WIMPs can be enhanced by the complementarity of dark matter searches and LHC and what are the consequences for theoretical motivated dark matter models. A particular focus will be on supersymmetric models in which the sneutrino can be the dark matter candidate. I will close on predictions and expectations for detection in a relatively close ...
The ALICE collaboration has presented new results on the production rates of antideuterons based on data collected at the highest collision energy delivered so far at the Large Hadron Collider. The antideuteron is composed of an antiproton and an antineutron. The new measurements are important because the presence of antideuterons in space is a promising indirect signature of dark matter candidates. The results mark a step forward in the search for dark matter.. Recent astrophysical and cosmological results point towards dark matter being the dominant form of matter in the universe, accounting for approximately 85% of all matter. The nature of dark matter remains a great mystery, and cracking its secrets would open a new door for physics.. Detecting antideuterons in space could be an indirect signature of dark matter, since they could be produced during the annihilation or decay of neutralinos or sneutrinos, which are hypothetical dark matter particles.. Various experiments are on the hunt for ...
Significance: Levels of platelet noncoding RNAs (ncRNAs) are altered by disease, and ncRNAs may exert functions inside and outside of platelets. Their role in physiologic hemostasis and pathologic thrombosis remains to be explored. Recent Advances: The number of RNA classes identified in platelets has been growing since the past decade. Apart from coding messenger RNAs, the RNA landscape in platelets comprises ncRNAs such as microRNAs, circular RNAs, long ncRNAs, YRNAs, and potentially environmentally derived exogenous ncRNAs. Recent research has focused on the function of platelet RNAs beyond platelets, mediated through protective RNA shuttles or even cellular uptake of entire platelets. Multiple studies have also explored the potential of platelet RNAs as novel biomarkers. Critical Issues: Platelet preparations can contain contaminating leukocytes. Even few leukocytes may contribute a substantial amount of RNA. As biomarkers, platelet RNAs have shown associations with platelet activation, but ...
Invitrogen). Normal meningeal RNA samples were purchased from BioChain and Analytical Biological Services, or extracted from normal…Normal meningeal genomic DNA samples were either purchased fromBioChain and Analytical Biological Services or extracted from normal ...
Imprinted genes play essential roles in development, and their allelic expression is mediated by imprinting control regions (ICRs). The Dlk1-Dio3 locus is among the few imprinted domains controlled by a paternally methylated ICR. The unmethylated maternal copy activates imprinted expression early in development through an unknown mechanism. We find that in mouse embryonic stem cells (ESCs) and in blastocysts, this function is linked to maternal, bidirectional expression of noncoding RNAs (ncRNAs) from the ICR. Disruption of ICR ncRNA expression in ESCs affected gene expression in cis, led to acquisition of aberrant histone and DNA methylation, delayed replication timing along the domain on the maternal chromosome, and changed its subnuclear localization. The epigenetic alterations persisted during differentiation and affected the neurogenic potential of the stem cells. Our data indicate that monoallelic expression at an ICR of enhancer RNA-like ncRNAs controls imprinted gene expression, ...
It is amazing that the team has managed to achieve such precision from only the first year of their survey, said National Science Foundation Program Director Nigel Sharp. Now that their analysis techniques are developed and tested, we look forward with eager anticipation to breakthrough results as the survey continues.. DES scientists used two methods to measure dark matter. First, they created maps of galaxy positions as tracers, and second, they precisely measured the shapes of 26 million galaxies to directly map the patterns of dark matter over billions of light-years, using a technique called gravitational lensing.. To make these ultraprecise measurements, the DES team developed new ways to detect the tiny lensing distortions of galaxy images, an effect not even visible to the eye, enabling revolutionary advances in understanding these cosmic signals. In the process, they created the largest guide to spotting dark matter in the cosmos ever drawn (see image). The new dark matter map is 10 ...
Numerical simulation showing the distribution of dark matter in a large volume of the universe. The box shown spans a distance of about 1 billion light-years. The structures are displayed so that the brighter regions have a higher density (that is, more dark matter) than the darker regions. The dark matter is concentrated into a web-like distribution of filaments that intersect at dense nodes where great clusters of galaxies are expected to form and become visible. At the rear of the cube (to the left), three blue disks represent three distant galaxies. The yellow lines that cross the box represent light rays from those galaxies propagating through the universe. In the absence of intervening matter, the light would travel on straight lines but in the presence of matter, the paths of the rays are evidently deflected by the gravitational effects of the clumpy matter (the breaks in the yellow lines illustrate the light passing behind a clump of dark matter). The light from a distant galaxy rarely ...
I know what dark matter is. Dark matter is the pit around a sandcastle. Yes, when you build a sandcastle in a flat beach, there is always a pit formed around it. That means, the density of a vacuum in that gravitational pit is lower than expected. On average, the density of matter in the space between the stars of the Milky Way is 0.1 neutral hydrogen atoms per cubic centimetre. In a gravitational pit around a galaxy (or a cluster of galaxies) the density of matter is drastically lower than that value, so there we have what we call dark matter. The rapidly formed clusters of matter in outer space produce deeper gravitational pits around them. If the formation of clusters of matter is slow, their gravitational pits are shallow. That explains the reason why some galaxies, or cluster of galaxies, dont exhibit great amounts of that alleged dark matter, but others do. So, a gravitational pit is a gravitational anti-well, If, by definition, we put the value of the gravitational potential of a flat ...
I know what dark matter is. Dark matter is the pit around a sandcastle. Yes, when you build a sandcastle in a flat beach, there is always a pit formed around it. That means, the density of a vacuum in that gravitational pit is lower than expected. On average, the density of matter in the space between the stars of the Milky Way is 0.1 neutral hydrogen atoms per cubic centimetre. In a gravitational pit around a galaxy (or a cluster of galaxies) the density of matter is drastically lower than that value, so there we have what we call dark matter. The rapidly formed clusters of matter in outer space produce deeper gravitational pits around them. If the formation of clusters of matter is slow, their gravitational pits are shallow. That explains the reason why some galaxies, or cluster of galaxies, dont exhibit great amounts of that alleged dark matter, but others do. So, a gravitational pit is a gravitational anti-well, If, by definition, we put the value of the gravitational potential of a flat ...
Show moreNon-protein-coding RNAs (ncRNAs) are RNA molecules that function directly at the level of RNA without translating into protein. They play important biological functions in all three domains of life, i.e. Eukarya, Bacteria and Archaea. To understand the working mechanisms and the functions of ncRNAs in various species, a fundamental step is to identify both known and novel ncRNAs from large-scale biological data.Large-scale genomic data includes both genomic sequence data and NGS sequencing data. Both types of genomic data provide great opportunity for identifying ncRNAs. For genomic sequence data, a lot of ncRNA identification tools that use comparative sequence analysis have been developed. These methods work well for ncRNAs that have strong sequence similarity. However, they are not well-suited for detecting ncRNAs that are remotely homologous. Next generation sequencing (NGS), while it opens a new horizon for annotating and understanding known and novel ncRNAs, also introduces many ...
Show moreNon-protein-coding RNAs (ncRNAs) are RNA molecules that function directly at the level of RNA without translating into protein. They play important biological functions in all three domains of life, i.e. Eukarya, Bacteria and Archaea. To understand the working mechanisms and the functions of ncRNAs in various species, a fundamental step is to identify both known and novel ncRNAs from large-scale biological data.Large-scale genomic data includes both genomic sequence data and NGS sequencing data. Both types of genomic data provide great opportunity for identifying ncRNAs. For genomic sequence data, a lot of ncRNA identification tools that use comparative sequence analysis have been developed. These methods work well for ncRNAs that have strong sequence similarity. However, they are not well-suited for detecting ncRNAs that are remotely homologous. Next generation sequencing (NGS), while it opens a new horizon for annotating and understanding known and novel ncRNAs, also introduces many ...
New discoveries and accelerating progresses in the field of noncoding RNAs (ncRNAs) continuously challenges our deep-rooted doctrines in biology and sometimes our imagination. A growing body of evidence indicates that ncRNAs are important players in oncogenesis. While a stunning list of ncRNAs has been discovered, only a small portion of them has been examined for their biological activities and very few have been characterized for the molecular mechanisms of their action. To date, ncRNAs have been shown to regulate a wide range of biological processes, including chromatin remodeling, gene transcription, mRNA translation and protein function. Dysregulation of ncRNAs contributes to the pathogenesis of a variety of cancers and aberrant ncRNA expression has a high potential to be prognostic in some cancers. Thus, a new cancer research era has begun to identify novel key players of ncRNAs in oncogenesis. In this review, we will first discuss the function and regulation of miRNAs, especially focusing on the
It is becoming increasingly evident that noncoding RNA (ncRNA) constitutes an important component of chromatin and that ncRNA has a critical role in organizing the chromatin architecture and epigenetic memory by acting as an interface with the chromatin modifying machinery. Xist is the only RNA that has been shown to regulate gene expression by modulating chromatin structure using a multilayered silencing pathway. Recent emerging evidence indicates that long ncRNAs such as Kcnq1ot1 and Air which map to the Kcnq1 and Igf2r imprinted gene clusters, respectively, mediate the transcriptional silencing of multiple genes by interacting with chromatin and recruiting the chromatin modifying machinery. Though there are some parallels in the mechanistic actions of Kcnq1ot1 and Air, they seem to differ greatly in the way they achieve the silencing of overlapping and nonoverlapping genes. By reviewing the latest available evidence, we propose that Kcnq1ot1 RNA itself seems to play a critical role in the ...
The interesting thing about nematodes is that their genomic organization of both snoRNAs and other ncRNAs is quite different from other animals, says Chen. In contrast to the genomes of other metazoans, where most snoRNAs are found in introns and are under the control of independent promoters, nematode snoRNA loci are both intergenic and intronic (with and without promoters). Interestingly, plant snoRNAs are primarily located in intergenic regions. Other ncRNA genes (i.e., non-snoRNA genes) are mainly located in intergenic regions in both plants and animals. But in nematodes, Chen s team found that many of these other ncRNA genes are located in the introns of host protein-coding genes and are under the control of independent promoter elements ...
The profiling approaches used in this study have led to several novel discoveries in rat genomics, VSMC and Ang II-mediated gene regulation. Because rats are a widely used model organism for research related to CVDs, diabetes mellitus, and other pathologies, it is imperative to analyze their transcriptome in-depth. Our annotation of novel transcripts significantly expands the existing number of known transcripts expressed in the rat genome, which, compared with the human and mouse genomes, remains less well annotated. We found that, similar to mouse and human, the rat genome contains lncRNAs that are less abundantly expressed than previously annotated rat transcripts.22 Notably, our studies revealed that the identified lncRNAs may function as host transcripts for small RNAs, such as miRNAs. Our analysis of the transcriptome and epigenome associated with H3K4me3 and H3K36me3 uncovered that Lnc-Ang362 is proximal to miR-221 and miR-222. Based on the enrichment of H3K4me3, which is at the TSS of ...
Hardy, Rowan S., Doig, Craig L., Hussain, Zahrah, OLeary, Mary, Morgan, Stuart A., Pearson, Mark J., Naylor, Amy, Jones, Simon W., Filer, Andrew, Stewart, Paul M., Buckley, Christopher D., Lavery, Gareth G., Cooper, Mark S. and Raza, Karim (2016). 11β-Hydroxysteroid dehydrogenase type 1 within muscle protects against the adverse effects of local inflammation. Journal of Pathology, 240 (4), pp. 472-483. Pearson, Mark J. and Jones, Simon W. (2016). Review:Long Noncoding RNAs in the Regulation of Inflammatory Pathways in Rheumatoid Arthritis and Osteoarthritis. Arthritis and Rheumatology, 68 (11), pp. 2575-2583. Pearson, Mark J., Philp, Ashleigh M., Heward, James A., Roux, Benoit T., Walsh, David A., Davis, Edward T., Lindsay, Mark A. and Jones, Simon W. (2016). Long Intergenic Noncoding RNAs Mediate the Human Chondrocyte Inflammatory Response and Are Differentially Expressed in Osteoarthritis Cartilage. Arthritis and Rheumatology, 68 (4), pp. 845-856. ...
The trouble is that while it isnt that hard to devise a dark matter model or modified gravity model that is consistent with a lot of observations made by astronomers, devising one that is consistent with all of the observations turns out to be devilishly hard. Some of the early, very simple version of each model, such as a model with a single kind of dark matter particle with a particular mass in the 100s of GeV (100 times the mass of a proton more or less), or an early toy model with a very simple modification of gravity, dont fit the data. The former generates the wrong shaped dark matter halos and has other problems at the galactic scale, even though it does a great job at the cosmological scale of the entire universes structure. The latter works fine at galactic scales, but fails in galactic clusters where it predicts effects that are too small (among other things ...
Matt Strassler [April 18, 2012] Its not easy to see dark matter, which makes up most of the matter in the universe. Its dark. And yet, there is one way that dark matter might, in a sense, shine. How? If dark matter is made from particles that are their own anti-particles (as is true for…
Scientists from MIPT, the Institute for Nuclear Research (INR) of the Russian Academy of Sciences, and Novosibirsk State University (NSU) have discovered that the proportion of unstable particles in the composition of dark matter in the days immediately after the Big Bang was no more than 2%-5%. Their study has been published in Physical Review D. The discrepancy between the cosmological parameters in the modern Universe and the Universe shortly after the Big Bang can be explained by the fact that the proportion of dark matter has decreased. We have now, for the first time, been able to calculate how much dark matter could have been lost and what the corresponding size of the unstable component would be, says a co-author of the study academician Igor Tkachev, Head of the Department of Experimental Physics at INR and a lecturer at MIPTs Department of Fundamental Interactions and Cosmology. Astronomers first suspected that there was a large proportion of hidden mass in the Universe back in ...
Cells display a set of RNA molecules at one time point, reflecting thus the cellular transcriptional steady state, configuring therefore its transcriptome. It is basically composed of two different classes of RNA molecules; protein-coding RNAs (cRNAs) and protein non-coding RNAs (ncRNAs). Sequencing of the human genome and subsequently the ENCODE project identified that more than 80% of the genome is transcribed in some type of RNA. Importantly, only 3% of these transcripts correspond to protein-coding RNAs, pointing that ncRNAs are as important or even more as cRNAs. ncRNAs have pivotal roles in development, differentiation and disease. Non-coding RNAs can be classified into two distinct classes according to their length; i.e., small (<200 nt="" and="" long="">200 nt) noncoding RNAs. The structure, biogenesis and functional roles of small non-coding RNA have been widely studied, particularly for microRNAs (miRNAs). In contrast to microRNAs, our current understanding
Continual discoveries on non-coding RNA (ncRNA) have changed the landscape of human genetics and molecular biology. Over the past ten years it has become clear that ncRNAs are involved in many physiological cellular processes and contribute to molecular alterations in pathological conditions. Several classes of ncRNAs, such as small interfering RNAs, microRNAs, PIWI-associated RNAs, small nucleolar RNAs and transcribed ultra-conserved regions, are implicated in cancer, heart diseases, immune disorders, and neurodegenerative and metabolic diseases. ncRNAs have a fundamental role in gene regulation and, given their molecular nature, they are thus both emerging therapeutic targets and innovative intervention tools. Next-generation sequencing technologies (for example SOLiD or Genome Analyzer) are having a substantial role in the high-throughput detection of ncRNAs. Tools for non-invasive diagnostics now include monitoring body fluid concentrations of ncRNAs, and new clinical opportunities include silencing
Having just returned from an EMBO organised conference on non-coding RNA (ncRNA), I am bursting with facts about non-coding RNA which may be of interest (or not) to some of you. ncRNAs are RNAs that have been transcribed from the genome but do not get translated into protein. There is a burgeoning interest in them mainly…
Recent studies have unveiled the numerous roles of non-coding RNAs (ncRNAs) highlighting the biological significance of these previously overlooked RNA species. NcRNAs and especially microRNAs (miRNAs) and, more recently, long ncRNAs (lncRNAs) are currently in the center of biological research; involved in a plethora of biological processes affecting cell homeostasis. miRNAs are considered post-transcriptional gene regulators enabling translational repression, mRNA degradation and gene silencing thus playing a major role in gene expression. They bind on their target usually by partial or complete base pairing on specific miRNA recognition elements (MREs) on mRNA as well as other non-coding RNA sequences such as lncRNAs. Recent findings have also revealed some of the cellular mechanisms involving lncRNAs. For instance, lncRNAs have been shown to be associated to chromatin remodeling; structural scaffolding of nuclear protein substructures; cell cycle regulation; binding to Polycomb repressive ...
Oral cancer is a multifactorial pathology and is characterized by the lack of efficient treatment and accurate diagnostic tools. This is mainly due the late diagnosis; therefore, reliable biomarkers for the timely detection of the disease and patient stratification are required. Non-coding RNAs (ncRNAs) are key elements in the physiological and pathological processes of various cancers, which is also reflected in oral cancer development and progression. A better understanding of their role could give a more thorough perspective on the future treatment options for this cancer type. This review offers a glimpse into the ncRNA involvement in oral cancer, which can help the medical community tap into the world of ncRNAs and lay the ground for more powerful diagnostic, prognostic and treatment tools for oral cancer that will ultimately help build a brighter future for these patients.
Biotagging, a genetically encoded toolkit in the zebrafish, reveals novel non-coding RNA players during neural crest and myocardium development ...
Two new studies report that x-rays emanating from the hearts of nearby galaxies and galaxy clusters could be signs of particles of dark matter decaying in space.. X-rays of a specific wavelength emanating from the hearts of nearby galaxies and galaxy clusters could be signs of particles of dark matter decaying in space, two independent teams of astronomers report. If that interpretation is correct, then dark matter could consist of strange particles called sterile neutrinos that weigh about 1/100 as much as an electron. However, some other researches are skeptical.. For decades, astronomers and astrophysicists have thought that some sort of mysterious dark matter must provide the gravity that keeps individual galaxies from falling apart. In fact, the current standard model of cosmology indicates that a typical galaxy forms within a vast clump, or halo, of dark matter whose gravity keeps the stars from flying out into space. However, scientists do not know what dark matter is, as they have never ...
LncRNAs are among the least well-understood of non-protein-coding RNAs. They were previously considered merely transcriptional noise [11] but have increasingly garnered attention in recent years. Newer studies have shown that lncRNAs are involved in EMT. For example, several lncRNAs can be involved in the regulation or activation of the WNT signaling pathway in the Twist-induced EMT process [20]. H19 can promote pancreatic cancer metastasis by derepressing let-7s suppression on its target HMGA2-mediated EMT [21]. However, to our knowledge, no previous study has focused on the microarray expression profile of lncRNAs in LECs during EMT. Thus, we conducted the current study to assess the role of lncRNAs in the development and progression of EMT in LECs from the perspective of lncRNA.. In this study, we chose the HLE B-3 cell line. It is a primary cell line of LECs that is immortalized via infection with an adenovirus 12-SV40 virus, and can be used to investigate HLE physiology and cataracts ...
TY - JOUR. T1 - Long noncoding RNA complementarity and target transcripts abundance. AU - Zealy, Richard W.. AU - Fomin, Mikhail. AU - Davila, Sylvia. AU - Makowsky, Daniel. AU - Thigpen, Haley. AU - McDowell, Catherine H.. AU - Cummings, James C.. AU - Lee, Edward S.. AU - Kwon, Sang Ho. AU - Min, Kyung Won. AU - Yoon, Je Hyun. PY - 2018/3. Y1 - 2018/3. N2 - Eukaryotic mRNA metabolism regulates its stability, localization, and translation using complementarity with counter-part RNAs. To modulate their stability, small and long noncoding RNAs can establish complementarity with their target mRNAs. Although complementarity of small interfering RNAs and microRNAs with target mRNAs has been studied thoroughly, partial complementarity of long noncoding RNAs (lncRNAs) with their target mRNAs has not been investigated clearly. To address that research gap, our lab investigated whether the sequence complementarity of two lncRNAs, lincRNA-p21 and OIP5-AS1, influenced the quantity of target RNA ...
The long noncoding RNA, TINCR, functions as a competing endogenous RNA to regulate PDK1 expression by sponging miR-375 in gastric cancer Zhaoliang Chen,1 Hong Liu,1 Huili Yang,1 Yukai Gao,1 Gongwen Zhang,1 Jiaojiao Hu2 1Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong, 2Department of Hematology, Zhongda Hospital, Southeast University, Nanjing, China Background: Accumulating evidence indicates that the long noncoding RNA, TINCR, plays a critical role in cancer progression and metastasis. However, the overall biological role and mechanisms of TINCR that were involved in human gastric cancer (GC) progression remain largely unknown.Methods: TINCR expression was measured in 56 paired tumor and adjacent nontumor tissue samples by real-time polymerase chain reaction (PCR). Insights of the mechanism of competitive endogenous RNAs (ceRNAs) were gained from bioinformatic analysis, luciferase assays. The effects of TINCR and miR-375 on GC cell apoptosis and proliferation were studied by RNA
The noncoding form of the steroid receptor RNA activator (SRA, AF092038, http://annolnc.cbi.pku.edu.cn/cases/SRA) has been reported to function as a noncoding RNA by Lanz et al. [41] and is the first lncRNA that has experimentally derived secondary structure, which was derived by Novikova et al. [42]. In the interactive secondary structure plot with vertebrate phyloP score as color overlay, it is easy to identify two conserved regions. One is a hairpin region from base 30 to 72 (Fig. 3a). With approximately 75% of bases colored red, this conserved sub-structure is clearly distinguishable from others. In fact, this region corresponds to the most conserved H2 sub-structure highlighted by Novikova et al. [42]. Site-directed mutagenesis of this region reduced the co-activation performance of SRA by 40% [43], suggesting the importance of lncRNA secondary structure on its function [44]. The other distinct region is a three-way junction hairpin sub-structure from base 506 to 555 with 78% colored red ...
The steroid receptor RNA activator gene (SRA1) generates two distinct entities. SRA RNA coactivates several NRs whereas SRA protein (SRAP) is suspected to regulate the activity of several transcription factors, including estrogen receptors (ER). Splicing of SRA intron-1 is the major event defining SRAP coding frame. Fully spliced, coding SRA and intron-1 retained, non-coding SRA coexist in breast cancer cells. The relative proportion between the two types of SRA RNA maintains a balance between two genetically linked entities, SRA and SRAP. In this study, a minigene model was used to demonstrate that the primary sequence of SRA exon-1-intron-1-exon-2 is sufficient for alternative splicing of SRA intron-1. In addition, a modified oligoribonucleotidic construct promotes SRA intron-1 retention in breast cancer cells. This oligoribonucleotide differentially alters estradiol-induced transcription of ER regulated genes. Together, results presented herein demonstrate that the SRA-SRAP balance, which can ...
Long non-coding RNAs (lncRNAs), representing a large proportion of non-coding transcripts across the human genome, are evolutionally conserved and biologically functional. At least one-third of the phenotype-related loci identified by genome-wide association studies (GWAS) are mapped to non-coding intervals. However, the relationships between phenotype-related loci and lncRNAs are largely unknown. Utilizing the 1000 Genomes data, we compared single-nucleotide polymorphisms (SNPs) within the sequences of lncRNA and protein-coding genes as defined in the Ensembl database. We further annotated the phenotype-related SNPs reported by GWAS at lncRNA intervals. Because prostate cancer (PCa) risk-related loci were enriched in lncRNAs, we then performed meta-analysis of two existing GWAS for discovery and an additional sample set for replication, revealing PCa risk-related loci at lncRNA regions. The SNP density in regions of lncRNA was similar to that in protein-coding regions, but they were less ...
Long noncoding RNA NEAT1 promotes cell proliferation and invasion by regulating hnRNP A2 expression in hepatocellular carcinoma cells Yuanyi Mang, Li Li, Jianghua Ran, Shengning Zhang, Jing Liu, Laibang Li, Yiming Chen, Jian Liu, Yang Gao, Gang Ren Department of Hepato-Biliary-Pancreatic Surgery, The Calmette Affiliated Hospital of Kunming Medical University, The First Hospital of Kunming, Kunming, Yunnan, People’s Republic of China Abstract: Growing evidence demonstrates that long noncoding RNAs (lncRNAs) are involved in the progression of various cancers, including hepatocellular carcinoma (HCC). The role of nuclear-enriched abundant transcript 1 (NEAT1), an essential lncRNA for the formation of nuclear body paraspeckles, has not been fully explored in HCC. We aimed to determine the expression, roles and functional mechanisms of NEAT1 in the proliferation and invasion of HCC. Based on real-time polymerase chain reaction data, we suggest that NEAT1 is upregulated in HCC tissues compared with
Brett Smith for redOrbit.com - Your Universe Online. According to astrophysicists, dark matter is the key to understanding the universe as it comprises 85 percent of all mass found in it and is suspected to have caused the growth of galaxies.. In a new study to be presented at the Royal Astronomical Societys National Astronomy Meeting, scientists from that countrys Durham University have found a possible explanation for why some dark matter didnt form galaxies in the early Universe - gas that would have created galaxy was sterilized by the heat from the first stars that formed in the Universe.. Ive been losing sleep over this for the last 30 years, said Carlos Frenk, Director of Durham Universitys Institute for Computational Cosmology. Dark matter is the key to everything we know about galaxies, but we still dont know its exact nature. Understanding how galaxies formed holds the key to the dark matter mystery.. According to theory, dark matter in the early Universe trapped interstellar ...
Delimiting distinct chromatin domains is essential for temporal and spatial regulation of gene expression. Within the X-inactivation centre region (Xic), the Xist locus, which triggers X-inactivation, is juxtaposed to a large domain of H3K27 trimethylation (H3K27me3). We describe here that developmentally regulated transcription of Tsix, a crucial non-coding antisense to Xist, is required to block the spreading of the H3K27me3 domain to the adjacent H3K4me2-rich Xist region. Analyses of a series of distinct Tsix mutations suggest that the underlying mechanism involves the RNA Polymerase II accumulating at the Tsix 3-end. Furthermore, we report additional unexpected long-range effects of Tsix on the distal sub-region of the Xic, involved in Xic-Xic trans-interactions. These data point toward a role for transcription of non-coding RNAs as a developmental strategy for the establishment of functionally distinct domains within the mammalian genome.
Transcriptomic analyses have identified tens of thousands of intergenic, intronic, and cis-antisense long noncoding RNAs (lncRNAs) that are expressed from mammalian genomes. Despite progress in functional characterization, little is known about the post-transcriptional regulation of lncRNAs and their half-lives. Although many are easily detectable by a variety of techniques, it has been assumed that lncRNAs are generally unstable, but this has not been examined genome-wide. Utilizing a custom noncoding RNA array, we determined the half-lives of ∼800 lncRNAs and ∼12,000 mRNAs in the mouse Neuro-2a cell line. We find only a minority of lncRNAs are unstable. LncRNA half-lives vary over a wide range, comparable to, although on average less than, that of mRNAs, suggestive of complex metabolism and widespread functionality. Combining half-lives with comprehensive lncRNA annotations identified hundreds of unstable (half-life | 2 h) intergenic, cis-antisense, and intronic lncRNAs, as well as lncRNAs showing
Full Text - Long noncoding RNAs (lncRNAs) are known to exert their effects to tumor progression. In this study, the role of the lncRNA GAS5 (growth arrest specific 5) was confirmed in reducing non-small cell lung cancer (NSCLC) cisplatin (DDP) resistance. In NSCLC tissue samples, GAS5 expression decreased significantly. Low GAS5 levels were positively correlated with NSCLC characteristics including TNM, tumor size and lymphatic metastasis. Functionally, GAS5 significantly reduced NSCLC/DDP cell migration, invasion and epithelial-mesenchymal transition (EMT) progression in vitro. In vivo, GAS5 upregulation inhibited remarkably NSCLC/DDP cell tumor growth. Mechanism analysis suggested that GAS5 was a molecular sponge of miR-217, inhibiting the expression of phospholysine phosphohistidine inorganic pyrophosphate phosphatase (LHPP). In conclusion, this study reveals that the GAS5/miR-217/LHPP pathway reduces NSCLC cisplatin resistance and that LHPP may serve as a potential therapeutic target
TY - JOUR. T1 - Long non-coding RNA (lncRNA) transcriptional landscape in breast cancer identifies LINC01614 as non-favorable prognostic biomarker regulated by TGFβ and focal adhesion kinase (FAK) signaling. AU - Vishnubalaji, Radhakrishnan. AU - Shaath, Hibah. AU - Elkord, Eyad. AU - Alajez, Nehad M.. PY - 2019/12/1. Y1 - 2019/12/1. N2 - Long non-coding RNAs (lncRNAs) represent a class of epigenetic regulators implicated in a number of physiological and pathological conditions. Herein, we characterized the lncRNA expression portrait from 837 patients with invasive breast cancer and 105 normals from the cancer genome atlas (TCGA), which revealed eighteen upregulated and forty-six downregulated lncRNAs. Clustering analysis revealed distinct lncRNA profile for the triple negative breast cancer (TNBC) and normal breast tissue, while less separation was observed among the HER2+HR+, HER2+HR−, HER2−HR+ molecular subtypes. LINC01614, and LINC01235 correlated with worse disease-free survival (DFS), ...
Most large elliptical galaxies are found in groups and clusters of galaxies, and are likely the product of the merger of two spiral galaxies. In such an environment, the dark matter halos can be stripped away by gravitational tidal force and added to other galaxies or the group as a whole. Therefore, it is difficult to determine how much dark matter the original galaxies had, and how much they have lost to the group as a whole through interactions with their environment.. The importance of the issue of the intrinsic amount of dark matter associated with an elliptical galaxy has recently increased owing to a report by an international team of astronomers led by Aaron Romanowsky of the University of Nottingham, United Kingdom. This team found little, if any evidence of dark matter in three relatively nearby elliptical galaxies. Two of these were in loose galaxy groups, and one was isolated. Their result, based on optical data from the 4.2 meter William Herschel Telescope on the Spanish island of ...
TY - JOUR. T1 - Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. AU - Goff, Loyal A.. AU - Groff, Abigail F.. AU - Sauvageau, Martin. AU - Trayes-Gibson, Zachary. AU - Sanchez-Gomez, Diana B.. AU - Morse, Michael. AU - Martin, Ryan D.. AU - Elcavage, Lara E.. AU - Liapis, Stephen C.. AU - Gonzalez-Celeiro, Meryem. AU - Plana, Olivia. AU - Li, Eric. AU - Gerhardinger, Chiara. AU - Tomassy, Giulio S.. AU - Arlotta, Paola. AU - Rinn, John L.. PY - 2015/6/2. Y1 - 2015/6/2. N2 - Long noncoding RNAs (lncRNAs) have been implicated in numerous cellular processes including brain development. However, the in vivo expression dynamics and molecular pathways regulated by these loci are not well understood. Here, we leveraged a cohort of 13 lncRNA-null mutant mouse models to investigate the spatiotemporal expression of lncRNAs in the developing and adult brain and the transcriptome alterations resulting from the loss of these lncRNA loci. We show that ...
Hepatocellular carcinoma (HCC) is a common malignant tumor with high fatality rate. Recent studies reported that up-regulation of long non-coding RNA antisense non-coding RNA in the INK4 locus (lncRNA ANRIL) was found in HCC tissues, and which could affect HCC cells biological processes. However, the potential molecular mechanism of ANRIL in HCC is still unclear. The study aimed to uncover the effect of ANRIL on HepG2 cells growth, migration and invasion. The knockdown expression vectors of ANRIL were transfected into HepG2 cells, and qRT-PCR, CCK-8, flow cytometry, Transwell and western blot assays were performed to analyze the effect of ANRIL on cell proliferation, apoptosis, migration and invasion. The relative expression of miR-191 was then examined in ANRIL knockdown vector transfected cells. These experiments were repeated again for exploring the effect of miR-191 on HepG2 cells. NF-κB and Wnt/β-catenin signaling pathways were examined by using western blot assay. Knockdown of ANRIL inhibited
Researchers have found a set of long non-coding RNAs (lncRNAs) - RNA molecules with no protein-coding capacity - that participate in the metastatic process of ovarian cancer cells.. Inhibiting one of these molecules, called DNM3OS, reduced migration and invasion, suggesting that targeting lncRNAs might be a viable approach for treating ovarian cancer.. The study, Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition, was published in the journal Nature Communications.. Metastasis, which refers to the spread of cancer cells, is a common occurrence in patients with ovarian cancer and occurs in as many as 80 percent of patients. Metastasis is dependent on the ability of cancer cells to undergo a process called epithelial-to-mesenchymal transition (EMT), which allows cells to detach from other cancer cells and enter circulation.. Recent studies have suggested that lncRNAs are involved in the metastatic process. These molecules are known to regulate gene ...
Zhang, Liu, Gao, Zhang, Zhang (2019) Long noncoding RNA XIST acts as a competing endogenous RNA to promote malignant melanoma growth and metastasis by sponging miR-217 Panminerva medica ...
Long Noncoding RNA (lncRNA) FOXD2-AS1 Promotes Cell Proliferation and Metastasis in Hepatocellular Carcinoma by Regulating MiR-185/AKT Axis - Related articles #918230
Spermatogenesis, which is the complex and highly regulated process of producing haploid spermatozoa, involves testis-specific transcripts. Recent studies have discovered that long noncoding RNAs (lncRNAs) are novel regulatory molecules that play important roles in various biological processes. However, there has been no report on the comprehensive identification of testis-specific lncRNAs in mice. We performed microarray analysis of transcripts from mouse brain, heart, kidney, liver and testis. We found that testis harbored the highest proportion of tissue-specific lncRNAs (11%; 1607 of 14,256). Testis also harbored the largest number of tissue-specific mRNAs among the examined tissues, but the proportion was lower than that of lncRNAs (7%; 1090 of 16,587). We categorized the testis-specific lncRNAs and found that a large portion corresponded to long intergenic ncRNAs (lincRNAs). Genomic analysis identified 250 protein-coding genes located near (≤ 10 kb) 194 of the loci encoding testis-specific
title: The long noncoding RNA LUCAT1 promotes tumorigenesis by controlling ubiquitination and stability of DNA methyltransferase 1 in esophageal squamous cell carcinoma, doi: 10.1016/j.canlet.2017.12.016, category: Article
Long Noncoding RNA HOTTIP Promotes Nasopharyngeal Cancer Cell Proliferation, Migration, and Invasion by Inhibiting miR-4301 - Order reprints #912728
Circulating Long Noncoding RNA as a Potential Target for Prostate 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.
Keywords: lengthy non-coding RNA (lncRNA) immunoprecipitation MS2 coat-binding proteins ribonucleoprotein complicated (RNP) RT-PCR biochemistry 1 Intro Recently it is becoming clear RGS12 a significant part of the transcriptome encodes gene items that tend unable to WP1130 become translated into protein. Such transcripts higher than ~200-nt in length are termed long non-coding RNAs (lncRNAs) and they may either lie in intergenic regions (lincRNAs) or overlap with protein-coding genes. That the number of lncRNAs encoded by the human genome likely far outstrips the number of protein-coding mRNAs [1] indicates that lncRNAs generally are the products of an impressive level of faulty transcription or alternatively serve yet-to-be-discovered cellular functions. Differentiating between these two possibilities requires the careful application of biochemical techniques. For those few lncRNAs that have an ascribed function [2] a combination of genetic and biochemical experiments has moved the field ...
XCI can occur randomly or by imprinting, this is where the paternal X chromosome is silenced in the preimplantation embryo and extraembryonic tissue. Random XCI occurs in the epiblast and can inactivate either the maternally or paternally inherited X chromosome, resulting is an active and inactive chromosome, which is transmitted to descendant cells. Some studies have analysed the random XCI in KS patients, and found that there is a skewed inactivation of one allele and this has been detected in a variety of cases. Many other studies have been conducted and this has led to skewed XCI ranges from around 10-40% of cases in KS patients[24]. The X-inactivation centre which initiates XCI contains the X (inactive) specific transcript (XIST). XIST encodes an untranslated RNA which can coat and silence the X chromosome. In addition to non-coding transcripts, XCI involves chromatin modifiers and factors of nuclear organisation. Together these lead to a changed chromatin structure and spatial ...
Year after year, researches keep it up their impossible mission-like struggle (without Tom Cruise, of course) to find the totally hypothetical substance (or whatever it may be) called dark matter! What would it be? In astronomy and cosmology, dark matter is a type of matter hypothesized to account for a large part of the total mass in the universe. Dark matter cannot be seen directly…
BACKGROUND:The long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is expressed highly in various types of tumors. Moreover, the tumor-initiating role of MALAT1 has been probed in the context of breast cancer. This study was set to investigate the regulatory role of MALAT1 on the chemosensitivity of breast cancer cells to taxanes (Tax) and adriamycin (Adr). MATERIAL AND METHODS:Following the measurement of MALAT1 expression in patients with breast cancer by means of qRT-PCR, the connection between the MALAT1 expression pattern and the prognosis of breast cancer patients as well as the molecular typing of breast cancer patients was analyzed using Kaplan-Meier survival analysis and receiver operating characteristic (ROC) curves. Next, the analysis between the expression of MALAT1 and the clinical symptoms of breast cancer patients was carried out. Subsequently, we generated taxane-resistant MCF-7 cells (MCF-7/Tax) and purchased Adr-resistant MCF-7 cells (MCF-7/Adr)
Scientists in the USA have found a novel noncoding gene that alters proliferation in cancer cells to help tumour development.. The team, at the University of Michigan in Ann Arbor, identified THOR (Testis-associated Highly-conserved Oncogenic long noncoding RNA) while investigating an unexplored area of the genome harbouring a class of genes called long non-coding RNAs (ribonucleic acid) (lncRNAs). These genes do not contain information to make proteins, therefore they have long been regarded as junk DNA. More recently, non-coding regions of the genome have proved to have diverse functions in health and disease.. The study, published in Cell, demonstrates that the newly discovered non-coding gene is highly conserved in different species, including humans, mice and zebrafish. Genes that are evolutionarily conserved are likely important for biological processes. The fact that we found THOR to be a highly conserved IncRNA was exciting, said Dr Arul Chinnaiyan, who led the team.. When the ...
Despite increasing evidence to indicate that long non-coding RNAs (lncRNAs) are novel regulators of immunity, there has been no systematic attempt to identify and characterise the lncRNAs whose expression are changed following the induction of the innate immune response. To address this issue, we have employed next generation sequencing data to determine the changes in the lncRNA profile in 4 human (monocytes, macrophages, epithelium and chondrocytes) and 4 mouse cells types (RAW 264.7 macrophages, bone marrow derived macrophages, peritoneal macrophages and splenic dendritic cells) following exposure to the pro-inflammatory mediators, lipopolysaccharide (LPS) or interleukin-1. We show differential expression of 204 human and 210 mouse lncRNAs, with positional analysis demonstrating correlation with immune related genes. These lncRNAs are predominantly cell-type specific, composed of large regions of repeat sequences and show poor evolutionary conservation. Comparison within the human and mouse
To evaluate the relevance of our chicken lncRNA set, we analyzed the gene expression profiles of the three classes putative lncRNA transcripts, new mRNAs and ambiguous RNAs and also compared the structural features of our lncRNAs with those of the mouse and human lncRNAs. As expected, the 2193 putative lncRNA genes are on average tenfold less expressed than the known or new protein-coding genes, and the ambiguous RNAs have an intermediate expression (Fig. 1b). This is in accordance with previous findings in mammals that showed that lncRNAs are far less expressed than protein-coding genes [6, 29-31]. Then, we characterized the structural features of these chicken putative lncRNA transcripts in comparison to the human and mouse lncRNAs available in Ensembl and compared them with the protein-coding RNAs available in Ensembl for these three species. Overall, the features observed for the chicken lncRNAs are consistent with those observed in mammals in the human and mouse ENCODE projects [6] ...
Long noncoding RNAs (lncRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retrieve specific lncRNAs with bound protein and DNA sequenc …
Non-coding RNAs constitute almost 98% of the human genome. Long non-coding RNA (lnc RNA) is a large class of this family where the RNA sequences are more than 200 nucleotides long and do not encode for proteins.
Heart development is a dynamic process that involves transcriptome expression changes and cis (enhancer and promoter activities) and trans (transcription factor binding) regulation. Much previous work has established the regulatory mechanisms in this process.1-3 As the importance of noncoding RNAs in regulating expression and epigenetic modifications is gaining recognition in heart development, researchers have discovered long noncoding RNA (lncRNA) that directly regulate heart development and disease.4,5 For example, the lncRNA Fendrr binds to the PRC2 and TrxG/MLL complex and acts as a modulator of chromatin signatures to regulate gene activity in mouse heart.6 The lncRNA Braveheart also interacts with a component of the PRC2 complex during cardiac commitment.7 Interestingly, lncRNAs have been implicated in common cardiac congenital abnormalities, such as ventricular septal defects.8 They have also been implicated in aberrant chromatin conformations in the region of enhancer, silencer, and ...
Purpose : The role of long noncoding RNAs (lncRNAs) in ocular angiogenesis is largely unknown. The purpose of the project is to identify human endothelial cell (EC)-specific lncRNAs and test their involvement in ocular angiogenesis. Methods : lncRNA profiling using ocular EC lines and non EC lines was performed to identify EC-specific lncRNAs. Quantitative RT-PCR and and bioinformatics analysis were used to confirm the microarray results, and test their involvement in angiogenesis. Various angiogenesis assays, including Matrigel assays and EC-fibroblast co-culture assays were used to study the candidate lncRNAs in angiogenesis. Results : We identified ~500 lncRNAs that are enriched more than 2 folds in primary endothelial cells (ECs) compared to non-EC cells. A list of the lncRNAs show a correlated expression profile with nearby coding mRNAs that are implicated in vascular development by functional enrichment analysis. For many of them, the EC-specific expression is more robust than their ...
The new millennium heralds an unanticipated surge of genomic information, most notably an expansive class of long noncoding RNAs (lncRNAs). These transcripts, which now outnumber all protein-coding genes, often exhibit the same characteristics as mRNAs (RNA polymerase II-dependent, 5 methyl-capped, multiexonic, polyadenylated); yet, they do not encode for stable, well-conserved proteins. Elucidating the function of all relevant lncRNAs in heart, vasculature, lung, and blood is essential for generating a complete interactome in these tissues. This is particularly evident because an increasing number of investigators perform RNA-sequencing experiments where, typically, annotated lncRNAs exhibit impressive changes in gene expression. How does one go about evaluating an lncRNA when the sequence of the transcript lends no insight into how it may function within a cell type? Here, we provide a brief overview for the rational study of lncRNAs.
Untranslated regionsEdit. Main articles: 5' UTR and 3' UTR. Untranslated regions (UTRs) are sections of the mRNA before the ... A 5' cap (also termed an RNA cap, an RNA 7-methylguanosine cap, or an RNA m7G cap) is a modified guanine nucleotide that has ... Messenger RNA (mRNA) is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they ... Small interfering RNA (siRNA)Edit. Main article: siRNA. In metazoans, small interfering RNAs (siRNAs) processed by Dicer are ...
"Small untranslated RNA antitoxin in Bacillus subtilis". J. Bacteriol. 187 (19): 6641-6650. doi:10.1128/JB.187.19.6641-6650.2005 ... It consists of a non-coding 222nt sRNA called RatA (RNA anti-toxin A) and a protein toxin named TxpA (Toxic protein A). RatA ... Lee JM, Zhang S, Saha S, Santa Anna S, Jiang C, Perkins J (December 2001). "RNA expression analysis using an antisense Bacillus ... Toxin-antitoxin system Hok/sok system RdlD RNA Bacillus subtilis BSR sRNAs Bacillus subtilis type I antitoxin SR6 Silvaggi JM, ...
... the RNA dependent RNA polymerase, three proteins - the triple gene block (TGB) 1, 2 and 3 - and the coat protein. The RNA is ... The 3' untranslated region is ~100 nucleotides in length. Viral replication is cytoplasmic. Entry into the host cell is ... This in turn produces a negative stranded template from which a series of subgenomic RNAs are generated. These subgenomic RNAs ... Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription is the method ...
UTR = untranslated region. The main function of RNA is to carry information of amino acid sequence from the genes to where ... They are transfer RNA (tRNA) and ribosomal RNA (rRNA). tRNA[change , change source]. Transfer RNA (tRNA) is a short molecule of ... RNA is physically different from DNA: DNA contains two intercoiled strands, but RNA only contains one single strand. RNA also ... Protein synthesis RNAs[change , change source]. Messenger RNA[change , change source]. The structure of a mature eukaryotic ...
Sledjeski DD, Whitman C, Zhang A (March 2001). "Hfq is necessary for regulation by the untranslated RNA DsrA". Journal of ... Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA ... MicX sRNA (formerly known as A10) is a small non-coding RNA found in Vibrio cholerae. It was given the name MicX as it has a ... The MicX RNA gene overlaps with VCA0943 - a gene coding for a maltose transporter permease - but the ribonuclease RNAase E ...
The vimentin 3′ UTR protein-binding region is an RNA element that contains a Y shaped structure which has been shown to have ... Bermano G, Shepherd RK, Zehner ZE, Hesketh JE (May 2001). "Perinuclear mRNA localisation by vimentin 3′-untranslated region ... Zehner ZE, Shepherd RK, Gabryszuk J, Fu TF, Al-Ali M, Holmes WM (August 1997). "RNA-protein interactions within the 3 ' ... untranslated region of vimentin mRNA". Nucleic Acids Research. 25 (16): 3362-3370. doi:10.1093/nar/25.16.3362. PMC 146884. PMID ...
Zehner ZE, Shepherd RK, Gabryszuk J, Fu TF, Al-Ali M, Holmes WM (August 1997). "RNA-protein interactions within the 3 ' ... untranslated region of vimentin mRNA". Nucleic Acids Research. 25 (16): 3362-70. doi:10.1093/nar/25.16.3362. PMC 146884. PMID ...
In both the 5'UTR and 3'UTR are X-linked RNA binding motifs. One of the three stable stem loops in the 3'UTR contained an X- ... linked RNA binding motif. There were no identified miRNA targets in either untranslated regions. Based on microarray data, ...
Wang S, Browning KS, Miller WA (July 1997). "A viral sequence in the 3'-untranslated region mimics a 5' cap in facilitating ... Barley yellow dwarf virus 5' UTR is a non-coding RNA element containing structural elements required for translation of the ... Guo L, Allen EM, Miller WA (May 2001). "Base-pairing between untranslated regions facilitates translation of uncapped, ... nonpolyadenylated viral RNA". Molecular Cell. 7 (5): 1103-1109. doi:10.1016/S1097-2765(01)00252-0. PMID 11389856. Malys N, ...
The L segment encodes a RNA-dependent RNA polymerase. Bennett RS, Gresko AK, Murphy BR, Whitehead SS (2011). "Tahyna virus ... The 3' and 5' untranslated regions (UTR) are complementary and highly conserved. The S segment encodes two proteins: the ... These enveloped viruses have a three-segmented negative-strand RNA genome. of approximately 13 kb in total length. The three ... RT-PCR methods are under development to detect viral RNA in cerebrospinal fluid samples of patients with encephalitis. Genetic ...
"Biased hypermutagenesis associated with mutations in an untranslated hairpin of an RNA virus". Journal of Virology. 78 (14): ... The turnip crinkle virus (TCV) core promoter hairpin (Pr) is an RNA element located in the 3' UTR of the viral genome that is ... required for minus strand RNA synthesis. The picture shown is not the TCV core promoter, but an upstream hairpin that is also ...
This polyprotein has methyl transferase, viral helicase and RNA dependent RNA polymerase domains. There are untranslated ... Negevirus is a taxon of non segmented, positive sense single stranded RNA viruses that have been isolated from mosquitoes and ...
3D is the RNA-dependent RNA polymerase (RdRP). 2B, 2C, and 3A are core viral proteins. The genome also codes for 4 capsid ... The 5' untranslated region contains an internal ribosomal entry site (Type I IRES). Covalently bonded to the 5' UTR is the ... forming a double-stranded RNA intermediate Upon transcription of the negative sense RNA, it needs to get primed in order to ... The VPg protein that is covalently linked to the 5' end of the RNA genome has 2 U's attached to it. The purpose of these U's is ...
1996). "The RNA 3' cleavage factors CstF 64 kDa and CPSF 100 kDa are concentrated in nuclear domains closely associated with ... Specifically, this protein binds GU-rich elements within the 3'-untranslated region of mRNAs. CSTF2 has been shown to interact ... This gene encodes a nuclear protein with an RRM (RNA recognition motif) domain. The protein is a member of the cleavage ... "Entrez Gene: CSTF2 cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa". Takagaki, Y; Manley J L (March 2000). "Complex ...
... untranslated region pseudoknot functions in coronavirus RNA replication". Journal of Virology. 73 (10): 8349-8355. doi:10.1128/ ... Other RNA families identified in the coronavirus include the coronavirus SL-III cis-acting replication element (CRE), the ... The Coronavirus 3′ UTR pseudoknot is an RNA structure found in the coronavirus genome. Coronaviruses contain 30 kb single- ... stranded positive-sense RNA genomes. The 3′ UTR region of these coronavirus genomes contains a conserved ~55 nucleotide ...
The biological function of these large (200+ nucleotides) and untranslated RNA is largely unknown. Based upon the few works ... The non-coding RNA were identified as antisense RNA and long non-coding RNAs (lncRNA), poorly understood classes of regulatory ... Another notable result showed that many non-coding RNAs are dynamically expressed, with many being initiated in 3' untranslated ... Further efforts found a genomically and evolutionary widespread new class of RNAs, called transcription initiation RNAs (tiRNA ...
The positive sense RNA genome of Flavivirus contains 5' and 3' untranslated regions (UTRs). The 5'UTRs are 95-101 nucleotides ... One of the products cleaved is a RNA-dependent RNA polymerase, responsible for the synthesis of a negative-sense RNA molecule. ... Cellular RNA cap structures are formed via the action of an RNA triphosphatase, with guanylyltransferase, N7-methyltransferase ... Henderson BR, Saeedi BJ, Campagnola G, Geiss BJ (2011). Jeang K (ed.). "Analysis of RNA binding by the Dengue virus NS5 RNA ...
Untranslated Region of the Dengue Virus Type 2 RNA That Modulate Translation and Replication". Journal of Biological Chemistry ... untranslated region of flavivirus RNAs and potential cyclization sequences". Journal of Molecular Biology. 198 (1): 33-41. doi: ... "A Viral Noncoding RNA Generated by cis-Element-Mediated Protection against 5′→3′ RNA Decay Represses both Cap-Independent and ... "Structural complexity of Dengue virus untranslated regions: cis-acting RNA motifs and pseudoknot interactions modulating ...
... strand RNA genome is replicated through a double-stranded RNA intermediate that is formed using viral RDRP (RNA-Dependent RNA ... There is an un-translated region (UTR) at both ends of the picornavirus genome. The 5' UTR is usually longer, being around 500- ... The mRNA encodes RNA dependent RNA polymerase. This polymerase makes complementary minus strands of RNA, then uses them as ... Genomic RNAs of picornaviruses possess multiple RNA elements and they are required for both negative and plus strand RNA ...
The 5'UAR interacts with the 3'UAR, which is located at the 3' UTR of the genome to form a long-range RNA-RNA interaction. The ... Flavivirus 5' UTR are untranslated regions in the genome of viruses in the genus Flavivirus. The Flavivirus positive-oriented, ... Filomatori, C. V. (2006-08-15). "A 5' RNA element promotes dengue virus RNA synthesis on a circular genome". Genes & ... "Long-Range RNA-RNA Interactions Circularize the Dengue Virus Genome". Journal of Virology. 79 (11): 6631-6643. doi:10.1128/JVI. ...
Predictions show several possible RNA stem loop formations in the untranslated regions of the mRNA. The FAM83A gene encodes for ...
These proteins include, but are not limited to cohesin, RNA polymerase, and CP190. The insulator element that is found in the ... The gypsy insulator can be found in the 5' untranslated region (UTR) of the retrotransposon element. Gypsy affects the ...
They are the most common determinant of RNA stability in mammalian cells. AU-rich elements Gruber, Andreas R; Fallmann Jörg; ... AREsite is a database of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). AU-rich elements are ... http://rna.tbi.univie.ac.at/AREsite v t e. ...
MicroRNAs can bind to the three prime untranslated region (3'UTR) of the target messenger RNA (mRNA). Binding of the miRNA can ... In molecular biology, miR-184 microRNA is a short non-coding RNA molecule. MicroRNAs (miRNAs) function as posttranscriptional ...
Five prime untranslated region MiRNA RNA-binding protein Three prime untranslated region Untranslated region Dassi, E; ... It includes basic annotation, phylogenetic conservation, binding sites for RNA-binding proteins and miRNA, cis-elements, RNA ... Through its intuitive web interface, it furthermore provides full access to a wealth of information that integrates RNA ... untranslated sequences (UTR) and UTR regulatory annotations. ...
RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA strand. Hydrogen bonds of the RNA-DNA ... The regulatory sequence before ("upstream" from) the coding sequence is called the five prime untranslated region (5'UTR); the ... small nuclear RNA (snRNA), or enzymatic RNA molecules called ribozymes as well as larger non-coding RNAs such as ribosomal RNA ... RNA synthesis by RNA polymerase was established in vitro by several laboratories by 1965; however, the RNA synthesized by these ...
Stem-loop Pseudoknot RNA Nucleic acid tertiary structure Three prime untranslated region Adaptation Adapted from Proteopedia ... Chen, Yu, and Varani, Gabriele(Jun 2010) RNA Structure. In: eLS. John Wiley & Sons Ltd, Chichester. "RNA Structure". ... RNA. 12 (10): 1893-906. doi:10.1261/rna.115606. PMC 1581982. PMID 16921068. "The Kissing-Loop Motif". Biomolecular Images and ... and intermolecular kissing interactions are important in forming the tertiary or quaternary structure of many RNAs. RNA kissing ...
Although individual snRNPs are believed to recognize specific nucleic acid sequences through RNA-RNA base pairing, the specific ... untranslated region. Additional splice variants have been described but sequences for the complete transcripts have not been ... RNA binding. Cellular component. • cytoplasm. • U5 snRNP. • catalytic step 2 spliceosome. • U4/U6 x U5 tri-snRNP complex. • ...
Second, there can be a bend in the DNA that will inhibit RNA processing. When located in the exon or the untranslated region, ... direction while the complementary RNA is synthesized in the 5' to 3' direction. RNA is similar to DNA, except that RNA contains ... RNA polymerase is prevented from transcribing the DNA sequence into RNA. With transcription blocked, the translation of RNA ... An important region for the activity of gene repression and expression found in RNA is the 3' untranslated region. This is a ...
Replication follows the double-stranded RNA virus replication model. Double-stranded RNA virus transcription is the method of ... Totiviruses contain a long 5' untranslated region (5' UTR) which functions as an internal ribosome entry site (IRES). ... and an RNA-dependent RNA polymerase (RdRp). The 5' end of the positive strand of the dsRNA genome has no cap and is very ... Totivirus is a genus of double-stranded RNA viruses in the family Totiviridae. Fungi serve as natural hosts. The name of the ...
除了蛋白質編碼基因之外,人類的基因組還包含了數千個RNA基因(製造非編碼RNA),其中包括用來轉錄轉運RNA(tRNA)、核糖體RNA(rRNA)與信使RNA(mRNA)的基因。其中轉錄rRNA的基因稱為rDNA,分佈在許多不同的染色體上。 ... such as untranslated regions, regulatory elements, non-protein-coding genes, and chromosomal
... the TATA box is found at RNA polymerase II promoter regions, although some in vitro studies have demonstrated that RNA ... untranslated region and bind to the TATA box to activate the transcription of oxidative stress related genes. ... "RNA polymerase III accurately initiates transcription from RNA polymerase II promoters in vitro". The Journal of Biological ... TATA-binding protein (TBP) can be recruited in two ways, by SAGA, a cofactor for RNA polymerase II, or by TFIID.[11] When ...
RNA binding. • acetyl-CoA C-acyltransferase activity. • long-chain-enoyl-CoA hydratase activity. ... 2003). "HADHB, HuR, and CP1 bind to the distal 3'-untranslated region of human renin mRNA and differentially modulate renin ... The encoded protein can also bind RNA and decreases the stability of some mRNAs. The genes of the alpha and beta subunits of ... untranslated region of human renin mRNA and differentially modulate renin expression". The Journal of Biological Chemistry. 278 ...
... untranslated leader sequence, definition of 18-bp polymorphisms, and differences with previous cDNA and amino acid sequences". ... and use of endonuclease digestion of PCR-amplified RNA to demonstrate lack of mRNA expression from the second allele". American ...
... each leading to different transcripts containing one of 8 untranslated 5' exons (I to VIII) spliced to the 3' encoding exon. ... RNA expression pattern. More reference expression data. Gene ontology. Molecular function. • receptor binding. • neurotrophin ...
L region is an untranslated leader region that gives the signal for packaging of the genome RNA. The 3' end includes 3 regions ... RNA: consists of a dimer RNA. It has a cap at the 5' end and a poly(A) tail at the 3' end. The RNA genome also has terminal ... These inserts are transcribed by enzymes of the host into new RNA molecules that enter the cytosol. Next, some of these RNA ... In most viruses, DNA is transcribed into RNA, and then RNA is translated into protein. However, retroviruses function ...
೪೧.೦ ೪೧.೧ Eddy SR (December 2001). "Non-coding RNA genes and the modern RNA world". Nat. Rev. Genet. 2 (12): 919-29. doi: ... Mignone, Flavio; Gissi, Carmela; Liuni, Sabino; Pesole, Graziano (2002-02-28). "Untranslated regions of mRNAs". Genome Biology ... ೯೦.೦ ೯೦.೧ Claverie JM (September 2005). "Fewer genes, more noncoding RNA". Science 309 (5740): 1529-30. Bibcode:2005Sci... ... Domingo, E; Escarmís, C; Sevilla, N; Moya, A; Elena, SF; Quer, J; Novella, IS; Holland, JJ (June 1996). "Basic concepts in RNA ...
... untranslated regions of viral mRNA. Some viruses (e.g. tobacco mosaic virus (TMV)) have RNA sequences that contain a "leaky" ... Instead, the naked viral RNA may alter the function of the cells through a mechanism similar to RNA interference, in which the ... The RNA carries genetic information to code for the production of new infectious particles. More recently virus research has ... This protein will act on the rest of the genome producing negative strand sub-genomic RNAs then act upon these to form positive ...
Byun CJ, Seo J, Jo SA, Park YJ, Klug M, Rehli M, Park MH, Jo I (January 2012). "DNA methylation of the 5'-untranslated region ... Briefly, ncRNAs are involved in signaling cascades with epigenetic marking enzymes such as HMTs, and/or with RNA interference( ... significantly increases SMN2 RNA/protein levels in spinal muscular atrophy cells". primary. Human Genetics. 120 (1): 101-10. ... non-coding RNA (ncRNA) function. Briefly, histone-mediated transcriptional control occurs by the wrapping of DNA around a ...
UTR = untranslated region. The main function of RNA is to carry information of amino acid sequence from the genes to where ... They are transfer RNA (tRNA) and ribosomal RNA (rRNA).. tRNA[change , change source]. Transfer RNA (tRNA) is a short molecule ... RNA is physically different from DNA: DNA contains two intercoiled strands, but RNA only contains one single strand. RNA also ... Protein synthesis RNAs[change , change source]. Messenger RNA[change , change source]. The structure of a mature eukaryotic ...
... and small amounts of the flanking untranslated regions and introns are analyzed. Therefore, although these tests are highly ...
Bamford RN, DeFilippis AP, Azimi N, Kurys G, Waldmann TA (May 1998). "The 5' untranslated region, signal peptide, and the ... double-stranded RNA, or lipopolysaccharide and promotes dendritic cell activation". Journal of Immunology. 167 (3): 1179-87. ... untranslated region (UTR), 486 bp coding sequence and the C-terminus 400 bp 3'-UTR region. The other isoform (IL-15 SSP) has a ...
Main article: Three prime untranslated region. Three prime untranslated regions (3'UTRs) of messenger RNAs (mRNAs) often ... RNAs are the direct products of genes, and these small RNAs can direct enzyme complexes to degrade messenger RNA (mRNA) ... These processed RNAs are incorporated into the RNA-induced silencing complex (RISC), which targets messenger RNA to prevent ... Two types of small ribonucleic acid (RNA) molecules - microRNA (miRNA) and small interfering RNA (siRNA) - are central to RNA ...
The term exon refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. In RNA ... In protein-coding genes, the exons include both the protein-coding sequence and the 5′- and 3′-untranslated regions (UTR). ... An exon is any part of a gene that will encode a part of the final mature RNA produced by that gene after introns have been ... The term later came to include sequences removed from rRNA[2] and tRNA,[3] and it also was used later for RNA molecules ...
At the 5′ and 3′ ends of the RNA are the untranslated regions (UTR), that are not translated into proteins but are important to ... RNA replication takes place via the viral RNA-dependent RNA polymerase NS5B, which produces a negative strand RNA intermediate ... is the viral RNA-dependent RNA polymerase. NS5B has the key function of replicating the HCV's viral RNA by using the viral ... HCV has a wide variety of genotypes and mutates rapidly due to a high error rate on the part of the virus' RNA-dependent RNA ...
The cytosolic GS gene translation is regulated by its 5' untranslated region (UTR), while its 3' UTR plays role in transcript ... These inactivating factors are furthermore regulated by different Non-coding RNAs: The sRNA NsiR4 interacts with the 5'UTR of ... "The 5' untranslated region of the soybean cytosolic glutamine synthetase β(1) gene contains prokaryotic translation initiation ...
Class I TEs are copied in two stages: first, they are transcribed from DNA to RNA, and the RNA produced is then reverse ... Surprisingly, the RNAi sequences are derived from the 5' untranslated region (UTR) of the LINE1, a long terminal which repeats ... Jin Y, Zhang W, Li Q (June 2009). "Origins and evolution of ADAR‐mediated RNA editing". IUBMB Life. 61 (6): 572-578. doi: ... TEs also serve to generate repeating sequences that can form dsRNA to act as a substrate for the action of ADAR in RNA editing ...
The 1544G-1651G haplotype in the 3'-Untranslated region of the DP2 gene increased the stability of the gene's mRNA; this ... DP2 messenger RNA is also expressed by human basophils, eosinophils, a subpopulation of cytotoxic T cells (i.e. CD8+ T cells), ...
doi:10.1261/rna.652807.. *↑ Slomovic, S.; Laufer, D; Geiger, D; Schuster, G (2006). "Polyadenylation of ribosomal RNA in human ... "Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites". Science 320 (5883 ... Edmonds, M. (1971). "Polyadenylic Acid Sequences in the Heterogeneous Nuclear RNA and Rapidly-Labeled Polyribosomal RNA of HeLa ... doi:10.1261/rna.46306.. *↑ 35,0 35,1 Meijer, H. A.; Bushell, M.; Hill, K.; Gant, T. W.; Willis, A. E.; Jones, P.; De Moor, C. H ...
Calmels C, Ventura M, Aknin C, Métifiot M, Andreola ML «De novo RNA synthesis catalyzed by the Zika Virus RNA polymerase domain ... untranslated region of Zika virus» (en anglès). Trop Med Int Health, 2017 Feb 18, pàgs: 20 prov. (article de subscripció). DOI ... Musso D, Richard V, Teissier A, Stone M, et al «Detection of ZIKV RNA in semen of asymptomatic blood donors» (en anglès). Clin ... Bingham, AM; Cone, M; Mock, V; Heberlein-Larson, L; et al «Comparison of Test Results for Zika Virus RNA in Urine, Serum, and ...
Toda K, Shizuta Y (April 1993). "Molecular cloning of a cDNA showing alternative splicing of the 5'-untranslated sequence of ... RNA expression pattern. More reference expression data. Gene ontology. Molecular function. • iron ion binding. • oxygen binding ...
An important region for the activity of gene repression and expression found in RNA is the 3' untranslated region. This is a ... RNA polymerase is prevented from transcribing the DNA sequence into RNA. With transcription blocked, the translation of RNA ... direction while the complementary RNA is synthesized in the 5' to 3' direction. RNA is similar to DNA, except that RNA contains ... 1: RNA Polymerase, 2: Repressor (LacI), 3: Promoter, 4: Operator, 5: Lactose, 6: lacZ, 7: lacY, 8: lacA. Top: lac operon is ...
Lazarov ME، Martin MM، Willardson BM، Elton TS (1999). "Human phosducin-like protein (hPhLP) messenger RNA stability is ... regulated by cis-acting instability elements present in the 3'-untranslated region.". Biochim. Biophys. Acta. 1446 (3): 253-64 ...
RNA splicing). Istilah ekson mengacu pada urutan DNA dalam gen dan urutan yang sesuai dalam transkrip RNA. Dalam penjalinan RNA ... Daerah yang tidak ditranslasi (untranslated region, UTR). Referensi[sunting , sunting sumber]. *^ Gilbert W (February 1978). " ... Istilah ini kemudian mencakup urutan yang dihapus dari rRNA[2] dan tRNA,[3] kemudian juga digunakan untuk molekul RNA yang ... Ekson dalam prekursor RNA duta (pre-mRNA). Ekson dapat mencakup urutan yang mengkode asam amino (merah) dan urutan yang tidak ...
There are DNA regions that are not transcribed as well as untranslated regions of the RNA.[5][6] ... 1. genes that are transcribed into RNAs and are translated into polypeptide chains.. 2. genes whose transcripts (tRNAs, rRNAs, ...
Davis DL, Burch JB (April 1992). "Isolation of a chicken HMG2 cDNA clone and evidence for an HMG2-specific 3'-untranslated ... RNA binding. Cellular component. • cytoplasm. • cell nucleus. • chromosome. Biological process. • multicellular organism ... untranslated region". Gene. 198 (1-2): 269-74. doi:10.1016/S0378-1119(97)00324-7. PMID 9370291.. ...
positive regulation of transcription from RNA polymerase II promoter. • positive regulation of SMAD protein import into nucleus ... "Inhibition of translation of transforming growth factor-beta 3 mRNA by its 5' untranslated region". Molecular and Cellular ...
... untranslated region (3UTR) is emerging as critically important in regulating gene expression at posttranscriptional levels. ... Aberrant regulation of messenger RNA 3-untranslated region in human cancer Cell Oncol. 2007;29(1):1-17. doi: 10.1155/2007/ ... The messenger RNA 3-untranslated region (3UTR) is emerging as critically important in regulating gene expression at ... RNA-binding proteins and non-coding RNAs). Alterations in any of these components can lead to disease. Here, we review the ...
RNA has been found in extracts of ascites carcinoma Krebs-2 cells. This was done using UV-irradiation on extracts supplemented ... A factor that specifically binds to the 5-untranslated region of encephalomyocarditis virus RNA FEBS Lett. 1990 Feb 26;261(2): ... A protein factor that specifically binds to the 5-untranslated region of encephalomyocarditis virus (EMCV) RNA has been found ... This set of transcripts has allowed us to find out that the factor (p58) binds to EMCV RNA within the sequence 315-485. ...
Cellular proteins bind to the poly(U) tract of the 3 untranslated region of hepatitis C virus RNA genome.. Luo G1. ... untranslated region (3 UTR) of the hepatitis C virus RNA genome. Two cellular proteins, with estimated molecular masses of 58 ... UTR RNA with deletion of the poly(U) tract competed out only p58 binding but not p35 binding, and (6) an RNA containing the ... UV cross-linking analyses were performed in an attempt to determine cellular protein-viral RNA interactions with the 3 ...
Mobility-shift assays using a control RNA detected an RNA-protein interaction that is lost with the patient RNA, and HuR was ... untranslated region variant in FMR1 eliminates neuronal activity-dependent translation of FMRP by disrupting binding of the RNA ... untranslated region variant in FMR1 eliminates neuronal activity-dependent translation of FMRP by disrupting binding of the RNA ... untranslated region variant in FMR1 eliminates neuronal activity-dependent translation of FMRP by disrupting binding of the RNA ...
... untranslated regions (UTRs). Scanning through the 5′UTR requires the adenosine triphosphate (ATP)-dependent RNA helicase ... Migration of Small Ribosomal Subunits on the 5′ Untranslated Regions of Capped Messenger RNA by Nikolay E. Shirokikh 1,*, Yulia ... "Migration of Small Ribosomal Subunits on the 5′ Untranslated Regions of Capped Messenger RNA." Int. J. Mol. Sci. 20, no. 18: ... untranslated regions (UTRs). Scanning through the 5′UTR requires the adenosine triphosphate (ATP)-dependent RNA helicase ...
The 3 untranslated region of picornavirus RNA: features required for efficient genome replication.. J B Rohll, D H Moon, D J ... The 3 untranslated region of picornavirus RNA: features required for efficient genome replication. ... The 3 untranslated region of picornavirus RNA: features required for efficient genome replication. ... The 3 untranslated region of picornavirus RNA: features required for efficient genome replication. ...
... untranslated region (3′UTR) is emerging as critically important in regulating gene expression at posttranscriptional levels. ... Abstract: The messenger RNA 3′-untranslated region (3′UTR) is emerging as critically important in regulating gene expression at ... Aberrant regulation of messenger RNA 3′-untranslated region in human cancer Article type: Research Article ... Keywords: Post-transcriptional gene regulation, RNA-binding proteins, non-coding RNAs, miRNAs, AU-rich elements (ARE), ...
Binding of the 5-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral ... untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and ... In a screen based on a yeast three-hybrid system using the 5-untranslated region (5-UTR) of SARS coronavirus (SARS-CoV) RNA ... Using small interfering RNA (siRNA) against MADP1, defective viral RNA synthesis was observed in the knockdown cells, therefore ...
The non-native 5′ untranslated enhancers may also be effective in many different types of transcription or translation systems ... untranslated sequences or artificial leader sequences. Preferably, commercially useful proteins, polypeptides, or fusion ... The present invention provides a method for enhancing the production of RNAs or proteins in a plant host using either non- ... The genomic RNA of a plus sense RNA virus is messenger sense, which makes the naked RNA infectious. Many plant viruses belong ...
RNA stability is regulated by posttranscriptional control through 3′-UTR of IL-10 mRNA. A, RNAs were isolated at different time ... Evidence of RNA-destabilizing activities in all three regions was deduced from luciferase reporter assays. The half-life of RNA ... B, To determine RNA half-life, the intensities of IL-10/Ig RNAs from nonstimulated IL-10/Ig no-UTR (▴), 6-h PMA-stimulated IL- ... Within the 6 h PMA-stimulated groups, the "no-UTR" RNA was more stable than "plus-UTR" RNA, suggesting that some mRNA ...
It is now evident that nonprotein coding RNA (ncRNA) plays a critical role in regulating the timing and rate of protein ... In the decade following the publication of the Human Genome, noncoding RNAs (ncRNAs) have reshaped our understanding of the ... Since small non-coding RNAs (including microRNAs) are implicated in the regulation of gene expression, we hypothesised that ... In this review, we discuss several examples of known RNA mechanisms for the regulation of protein synthesis. ...
Until recently, the genome-wide annotation of 3 untranslated regions received less attention than coding regions and the ... Direct RNA Sequencing technology from Helicos Biosciences which locates 3 polyadenylation sites to within +/- 2 nt, were ... clearer interpretation of small RNA expression and (4) identification of novel genes. While the specific examples displayed ... combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1) gene and ...
Main article: Three prime untranslated region. Three prime untranslated regions (3UTRs) of messenger RNAs (mRNAs) often ... RNA silencing also gets regulated[edit]. The same way that RNA silencing regulates downstream target mRNAs, RNA silencing ... doi:10.1261/rna.5235104. PMC 1370948. PMID 14970398.. *^ Zhou H, Hu H, Lai M (Dec 2010). "Non-coding RNAs and their epigenetic ... small interfering RNA (siRNA)[edit]. Main article: Small interfering RNA. siRNAs act in the nucleus and the cytoplasm and are ...
... untranslated (3′UTR) regions which are composed of two regions, one region from an 3′ untranslated region of a stable ... Eukaryotic messenger RNA (mRNA) contains three regions, 5′ untranslated region (5′UTR), protein coding region, and 3′ ... RNA), and analogs of either DNA or RNA, mRNA, and cDNA, such as PNA. The recombinant nucleic acid of the present inventions are ... untranslated region of a stable eukaryotic NA, and another region from the downstream end of an 3′ untranslated region of a ...
Untranslated regionsEdit. Main articles: 5 UTR and 3 UTR. Untranslated regions (UTRs) are sections of the mRNA before the ... A 5 cap (also termed an RNA cap, an RNA 7-methylguanosine cap, or an RNA m7G cap) is a modified guanine nucleotide that has ... Messenger RNA (mRNA) is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they ... Small interfering RNA (siRNA)Edit. Main article: siRNA. In metazoans, small interfering RNAs (siRNAs) processed by Dicer are ...
T1 - Interaction of RNA-binding proteins HuR and AUF1 with the human ATF3 mRNA 3′-untranslated region regulates its amino acid ... Interaction of RNA-binding proteins HuR and AUF1 with the human ATF3 mRNA 3′-untranslated region regulates its amino acid ... Interaction of RNA-binding proteins HuR and AUF1 with the human ATF3 mRNA 3′-untranslated region regulates its amino acid ... Pan, YX, Chen, H & Kilberg, MS 2005, Interaction of RNA-binding proteins HuR and AUF1 with the human ATF3 mRNA 3′-untranslated ...
Fingerprint Dive into the research topics of Structure of the 5= untranslated region of enteroviral genomic RNA. Together ...
Untranslated regions (5 UTR and 3 UTR). Untranslated regions (UTRs) are sections of the mRNA before the start codon and after ... A 5 cap (also termed an RNA cap, an RNA 7-methylguanosine cap or an RNA m7G cap) is a modified guanine nucleotide that has ... Some of the elements contained in untranslated regions form a characteristic secondary structure when transcribed into RNA. ... Splicing is usually performed by an RNA-protein complex called the spliceosome, but some RNA molecules are also capable of ...
CspA can bind to single-stranded DNA and RNA without high sequence specificity and has been proposed to function as an RNA ... Mutation Analysis of the 5′ Untranslated Region of the Cold Shock cspA mRNA of Escherichia coli Kunitoshi Yamanaka, Masanori ... Isolation of RNA and primer extension. E. coli AR137 harboring different plasmids was grown under the same conditions used for ... It is thus possible that the 5′-UTR of the cspA mRNA might act as an RNA thermometer, as was recently proposed for the rpoHmRNA ...
BNT162b2 protects the lower respiratory tract against the presence of viral RNA and shows no evidence of disease enhancement. ... that contain nucleoside-modified messenger RNA that encodes immunogens derived from the spike glycoprotein (S) of SARS-CoV-2, ... a, Structure of BNT162b1 and BNT162b2 RNA. UTR, untranslated region; SP, signal peptide. The proline subsitutions of S(P2) ( ... BNT162b1 RNA and BNT162b2 RNA). Heights of bars indicate the means of technical triplicates. b, Localization of BNT162b1 RNA- ...
UTRs with widely profiled RNA sequencing (RNA-seq) data. With this approach, the 3 UTR usage estimated from RNA-seq was found ... Hence, the computational RNA-seq method for the estimation of the 3 UTR landscape would be useful as a tool for studying not ... they contain complex RNA-biochemical experimental steps, resulting in a low yield of products. Now, researchers from Hanyang ... untranslated region (3 UTR) of mRNA contains elements that play regulatory roles in polyadenylation, localization, translation ...
Main article: Three prime untranslated region. Three prime untranslated regions (3UTRs) of messenger RNAs (mRNAs) often ... RNAs are the direct products of genes, and these small RNAs can direct enzyme complexes to degrade messenger RNA (mRNA) ... These processed RNAs are incorporated into the RNA-induced silencing complex (RISC), which targets messenger RNA to prevent ... Two types of small ribonucleic acid (RNA) molecules - microRNA (miRNA) and small interfering RNA (siRNA) - are central to RNA ...
Vodka! Speculating on purposes of untranslated RNA transcripts. In eukaryotic organisms and especially humans, large amounts of ... The supposed junk DNA that transcribes to supposed junk RNA is not junk at all. I recently discovered Read More… ... the DNA are transcribed into RNAs that never end up getting translated into proteins. This has led some to argue human DNA is ...
Untranslated regions. Main articles: 5 UTR and 3 UTR. Untranslated regions (UTRs) are sections of the RNA before the start ... A 5 cap (also termed an RNA cap, an RNA 7-methylguanosine cap or an RNA m7G cap) is a modified guanine nucleotide that has ... RNA messaggero he:MRNA la:MRNA lt:IRNR nl:Messenger RNA sk:Mediátorová ribonukleová kyselina sv:Budbärar-RNA uk:Матрична ... Some of the elements contained in untranslated regions form a characteristic secondary structure when transcribed into RNA. ...
Cis-regulatory elements play a number of important roles in determining the fate of messenger RNAs (mRNAs). Due to these ... untranslated regions. dsRNA. double-strand RNA. log. logistic regression. mRNA. messenger RNA ... M. Andronescu, V. Bereg, H.H. Hoos, A. Condon: RNA STRAND: The RNA secondary structure and statistical analysis database, BMC ... A. Taneda: An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery ...
Phosphorodiamidate morpholino targeting the 5′ untranslated region of the ZIKV RNA inhibits virus replication.. ... Phosphorodiamidate morpholino targeting the 5′ untranslated region of the ZIKV RNA inhibits virus replication.. ...
This is also the case in L. pneumophila where three sRNAs (RsmY, RsmZ, and 6S RNA) were recently shown to be important ... This is also the case in L. pneumophila where three sRNAs (RsmY, RsmZ and 6S RNA) were recently shown to be important ... In the past few years, the importance of regulation of virulence factors by small regulatory RNA (sRNAs) has been increasingly ... In the past few years, the importance of regulation of virulence factors by small regulatory RNA has been increasingly ...
... untranslated region of the mRNA. Another use of synthetic nucleotides is as primers (DNA or RNA) for a polymerase chain ... The term "antisense RNA" is used to mean an RNA nucleotide sequence (for example that encoded by an antisense DNA or ... "Foreign gene products" are RNA or proteins encoded by "foreign genes" and "endogenous gene products" are RNA or proteins ... that encode genetic information for the synthesis of a whole RNA, a whole protein, or any portion of such whole RNA or whole ...
double-stranded RNA;. GFP,. green fluorescent protein;. PFR,. paraflagellar rod;. 5′ UTR,. 5′ untranslated region. ... RNA Synthesis and Transfection.. RNA was synthesized from linear DNA templates by using the Ampliscribe T7 RNA polymerase kit ... To test our hypothesis, we transfected procyclic trypanosomes with RNA made in vitro with T7 RNA polymerase. RNA extending from ... or to RNA-mediated RNA degradation in plants (18).. From a cell biology point of view, FAT RNA-mediated destruction of α- ...
RNA modifications impact numerous cellular processes such as pre-mRNA splicing and protein synthesis. The elucidation of the ... RNA modifications impact numerous cellular processes such as pre-mRNA splicing and protein synthesis. The elucidation of the ... Here, we present a detailed procedure that allows the detection and quantification of RNA base modifications. This procedure ... impact cellular processes necessitates the ability to both detect and quantify the presence of these modifications within RNA ...
  • The 3'UTR governs gene expression via orchestrated interactions between mRNA structural components (cis-elements) and specific trans-acting factors (RNA-binding proteins and non-coding RNAs). (nih.gov)
  • Cellular proteins bind to the poly(U) tract of the 3' untranslated region of hepatitis C virus RNA genome. (nih.gov)
  • Interaction of these cellular proteins with the HCV 3' UTR is probably involved in regulation of translation and/or replication of the HCV RNA genome. (nih.gov)
  • Coronaviruses RNA synthesis occurs in the cytoplasm and is regulated by host cell proteins. (ntu.edu.sg)
  • RNA has been largely investigated within its role as an intermediary in the translation of genes into proteins. (wikipedia.org)
  • Pan, YX , Chen, H & Kilberg, MS 2005, ' Interaction of RNA-binding proteins HuR and AUF1 with the human ATF3 mRNA 3′-untranslated region regulates its amino acid limitation-induced stabilization ', Journal of Biological Chemistry , vol. 280, no. 41, pp. 34609-34616. (illinois.edu)
  • Messenger ribonucleic acid (mRNA) is a class of ribonucleic acid (RNA) molecules that serve as chemical "blueprints" for the production of proteins , carrying the coding information from a DNA template to the ribosomes , where the transcription into proteins takes place. (newworldencyclopedia.org)
  • The stability of mRNAs may be controlled by the 5' UTR and/or 3' UTR due to varying affinity for RNA degrading enzymes called ribonucleases and for ancillary proteins that can promote or inhibit RNA degradation. (newworldencyclopedia.org)
  • In eukaryotic organisms and especially humans, large amounts of the DNA are transcribed into RNAs that never end up getting translated into proteins. (uncommondescent.com)
  • RREs are defined by characteristic sequence motifs that serve as docking sites for trans-acting factors, such as short non-coding regulatory RNAs (e.g. microRNAs) and RNA binding proteins (RBPs) 2 . (nature.com)
  • mRNA-protein interactions drive this post-transcriptional regulation, yet knowledge of RNA binding proteins (RBP) in axons is limited. (mcponline.org)
  • A systematic assessment of axonal mRNAs interacting with hnRNP H1, hnRNP F, and hnRNP K, proteins that bound with high specificity to Nrn1 and Hmgb1 , revealed that axonal mRNAs segregate into axon growth-associated RNA regulons based on hnRNP interactions. (mcponline.org)
  • RNA binding proteins (RBPs) interacting with structural motifs within these mRNAs drive these post-transcriptional mechanisms ( 5 ). (mcponline.org)
  • The main function of RNA is to carry information of amino acid sequence from the genes to where proteins are assembled on ribosomes in the cytoplasm . (wikipedia.org)
  • Two kinds of non-coding RNAs help in the process of building proteins in the cell. (wikipedia.org)
  • Small nuclear RNAs ( snRNA ) join with proteins to form spliceosomes . (wikipedia.org)
  • acting oligonucleotide elements that interact with binding proteins and noncoding RNAs (micro ribonucleic acids - miRNAs and long noncoding ribonucleic acids - lncRNAs) through a combination of primary and secondary structures. (els.net)
  • Previous studies have confirmed that circRNAs may control gene transcription by isolating target microRNAs (miRNAs) and regulating RNA binding proteins, thus functioning as 'miRNA sponges' ( 9 ). (spandidos-publications.com)
  • The genome RNA serves as both mRNA for translation of viral proteins and the template for RNA replication. (clinsci.org)
  • Although structural proteins are clearly dispensable for RNA replication, recent evidence points to an important role of several non-structural proteins in particle assembly and release, turning their designation on its head. (clinsci.org)
  • Here, we study a collection of 75 CLIP-Seq experiments mapping the RNA binding sites for a diverse set of 51 human proteins to explore the role of TEs in post-transcriptional regulation of human mRNAs and lncRNAs via RNA-protein interactions. (biomedcentral.com)
  • We detect widespread interactions between RNA binding proteins (RBPs) and many families of TE-derived sequence in the CLIP-Seq data. (biomedcentral.com)
  • We present GraphProt, a computational framework for learning sequence- and structure-binding preferences of RNA-binding proteins (RBPs) from high-throughput experimental data. (biomedcentral.com)
  • The IRE is a stem-loop structure within the untranslated regions of mRNAs that encode proteins involved in cellular iron metabolism. (wikipedia.org)
  • The technique allows researchers to directly observe individual messenger RNA molecules (mRNAs) as they are translated into proteins in living cells. (healthcanal.com)
  • To visualize translation, Dr. Singer and his colleagues took advantage of a key occurrence during the first round of translation: the ribosome to which mRNAs attach must displace so-called RNA-binding proteins from the mRNAs. (healthcanal.com)
  • Cis -regulatory elements play a number of important roles in determining the fate of messenger RNAs (mRNAs). (springer.com)
  • Thus far, gRNA mediated RNA editing has been found only in the mitochondria of kinetoplastids , in which mRNAs are edited by inserting or deleting stretches of uridylates (Us). (wikidoc.org)
  • MicroRNAs (miRNAs) interact with target sites located in 3' untranslated regions (3'UTR) of mRNAs to down-regulate their expression when the appropriate miRNA is bound to target mRNA. (pubmedcentralcanada.ca)
  • Eukaryotic messenger ribonucleic acids (mRNAs) possess a tripartite structure that comprises a 5′ untranslated region, a coding region made up of the amino acid coding triplet codons and a 3′ untranslated region. (els.net)
  • Chatterjee S and Pal JK (2009) Role of 5′‐ and 3′‐untranslated regions of mRNAs in human diseases. (els.net)
  • Mignone F, Gissi C, Liuni S and Pesole G (2002) Untranslated regions of mRNAs. (els.net)
  • Cis-acting regulatory sequence elements are sequences contained in the 3′ and 5′ untranslated region, introns, or coding regions of precursor RNAs and mature mRNAs that are selectively recognized by a complementary set of one or more trans-acting factors to regulate posttranscriptional gene expression. (intechopen.com)
  • Schuster, Gadi 2004-10-06 00:00:00 A general characteristic of the 3′-untranslated regions (3′ UTRs) of plastid mRNAs is an inverted repeat (IR) sequence that can fold into a stem-loop structure. (deepdyve.com)
  • While modifications are best characterized in short, noncoding RNAs such as tRNAs, growing evidence indicates that mRNAs and long noncoding RNAs ( lncRNAs ) are likewise modified. (plantcell.org)
  • We find this type of modifications primarily within uncapped, degrading mRNAs and lncRNAs , suggesting they are the cause or consequence of RNA turnover. (plantcell.org)
  • Thus, the majority of the early research in molecular and cellular biology was focused on the protein-coding genes and their transcripts, messenger RNAs (mRNAs). (mdpi.com)
  • Localized in cytoplasmic mRNP granules containing untranslated mRNAs. (abcam.com)
  • The total RNAs were extracted from these samples and subjected to Clariom D microarray assays to detect the differentially expressed circRNAs and mRNAs. (medscimonit.com)
  • Hierarchical clustering analyses on these RNAs and their predicted mRNA targets showed that the majority of differentially expressed circRNAs and mRNAs had been up-regulated in the bladder tumors. (medscimonit.com)
  • UV cross-linking analyses were performed in an attempt to determine cellular protein-viral RNA interactions with the 3' untranslated region (3' UTR) of the hepatitis C virus RNA genome. (nih.gov)
  • The 3' untranslated region of picornavirus RNA: features required for efficient genome replication. (asm.org)
  • In a screen based on a yeast three-hybrid system using the 5'-untranslated region (5'-UTR) of SARS coronavirus (SARS-CoV) RNA as bait against a human cDNA library derived from HeLa cells, we found a positive candidate cellular protein, zinc finger CCHC-type and RNA-binding motif 1 (MADP1), to be able to interact with this region of the SARS-CoV genome. (ntu.edu.sg)
  • Correct and complete annotation in addition to the underlying genomic sequence is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. (semanticscholar.org)
  • To the extent it is useful to craft a distinction between these related concepts, RNA silencing may be thought of as referring to the broader scheme of small RNA related controls involved in gene expression and the protection of the genome against mobile repetitive DNA sequences, retroelements, and transposons to the extent that these can induce mutations. (wikipedia.org)
  • [6] When the dsRNA is exogenous (coming from infection by a virus with an RNA genome or laboratory manipulations), the RNA is imported directly into the cytoplasm and cleaved to short fragments by Dicer. (wikipedia.org)
  • The initiating dsRNA can also be endogenous (originating in the cell), as in pre-microRNAs expressed from RNA-coding genes in the genome. (wikipedia.org)
  • The number of ncRNAs encoded within the genome is unknown, however recent transcriptomic and microarray studies suggest the existence of over 30,000 long ncRNAs and at least as many small regulatory RNAs within the mouse genome alone. (wikidoc.org)
  • The non-translated regions at the genome ends of RNA viruses serve diverse functions and can exhibit various levels of nucleotide (nt) heterogeneity. (springer.com)
  • Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 platform for in situ high-content functional analysis of RREs. (nature.com)
  • This study provides a genome editing-based multiplex strategy for direct functional interrogation of RNA cis -regulatory elements in a native cellular environment. (nature.com)
  • Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2. (bvsalud.org)
  • Considering the possible importance of these regions in host mediated regulation of viral RNA genome , we wanted to explore the phenomenon. (bvsalud.org)
  • Thus, the 5' and 3'UTRs of DTMUV enable this virus to use a cap- and IRES-independent RNA genome translation strategy that is important for its propagation and virulence .IMPORTANCE Genus Flavivirus includes major human pathogens as well as animal -infecting viruses with zoonotic potential. (bvsalud.org)
  • Its genome is linear and is 7,293 nucleotides in length with both a 5' and 3' untranslated region and encodes its own 3' poly-A tail. (wikipedia.org)
  • The viral genome encodes for a poly-A tail, which can be recognized by cellular initiation factors and ribosomal subunits which kick starts the transcription process to make the negative-sense strand, forming a double-stranded RNA intermediate Upon transcription of the negative sense RNA, it needs to get primed in order to start making more positive sense RNA genome. (wikipedia.org)
  • The VPg protein that is covalently linked to the 5' end of the RNA genome has 2 U's attached to it. (wikipedia.org)
  • RNA-Seq was conducted and reads were mapped to the mouse reference genome (mm10) using HISAT. (biomedcentral.com)
  • With the advent of transcriptomic studies, it was revealed that only 2% of the genome has protein-coding capacity [ 1 , 2 ], and the vast majority of transcripts that do not have protein coding capacity are called non-coding RNAs (ncRNAs). (biomedcentral.com)
  • A positive-strand RNA virus of the Flaviviridae family, HCV contains a single-stranded RNA genome of approx. (clinsci.org)
  • Cis -acting RNA elements within the genome regulate RNA replication by forming secondary structures that interact with each other and trans -acting factors. (clinsci.org)
  • In particular, the ENCODE project has provided researchers with a genome-wide map of histone modification, DNase I hypersensitive sites, formaldehyde-assisted isolation of regulatory elements, transcription factor binding sites, RNA-seq and replication timing data across a number of cell lines ( 8 ). (spandidos-publications.com)
  • Over the past 8 years, more than 100 sRNAs have been discovered in Escherichia coli , and it is estimated that 200 to 300 such RNAs are present in an average bacterial genome ( 19 ). (asm.org)
  • It consists of a non-coding 222nt sRNA called RatA (RNA anti-toxin A) and a protein toxin named TxpA (Toxic protein A). RatA was discovered in intergenic regions of the B. subtilis genome, in a 728-nucleotide region between genes yqdB (later renamed TxpA) and yqbM. (wikipedia.org)
  • Our meta-analysis suggests a widespread role for TEs in shaping RNA-protein regulatory networks in the human genome. (biomedcentral.com)
  • Since small non-coding RNAs (including microRNAs) are implicated in the regulation of gene expression, we hypothesised that longevity of centenarians may reflect alterations in small non-coding RNA expression. (isharonline.org)
  • RNA silencing or RNA interference refers to a family of gene silencing effects by which gene expression is negatively regulated by non-coding RNAs such as microRNAs . (wikipedia.org)
  • Non-coding RNA genes include transfer RNA ( tRNA ) and ribosomal RNA ( rRNA ), small RNAs such as snoRNAs, microRNAs, siRNAs and piRNAs and lastly long ncRNAs that include examples such as Xist, Evf, Air, CTN and PINK. (wikidoc.org)
  • MicroRNAs (miRNAs), ∼22-nt-long noncoding RNAs, have recently emerged as key posttranscriptional regulators, controlling diverse biological processes, including responses to non-self. (rupress.org)
  • RNA editing in the precursor microRNAs (pre-miRNAs) of ath-miR854 family, resulting in secondary structure transformation, implies its potential role in microRNA (miRNA) maturation. (biomedcentral.com)
  • This length is somewhat arbitrary, but it serves to distinguish them from shorter, biologically distinct noncoding RNAs, such as microRNAs. (jci.org)
  • MicroRNAs imperfectly pair with untranslated regions of RNA and mediat. (bio-medicine.org)
  • MicroRNAs are a member of the family of small RNAs, the so-called dark matter of the biological world. (bio-medicine.org)
  • MicroRNAs imperfectly pair with untranslated regions of RNA and mediate translational repression and mRNA degradationhallmarks of the gene expression process. (bio-medicine.org)
  • RNA polymerase transcribes primary transcript mRNA (known as pre-mRNA ) into processed, mature mRNA. (wikipedia.org)
  • During transcription, RNA polymerase makes a copy of a gene from the DNA to mRNA as needed. (wikipedia.org)
  • One notable difference, however, is that eukaryotic RNA polymerase associates with mRNA-processing enzymes during transcription so that processing can proceed quickly after the start of transcription. (wikipedia.org)
  • Shortly after the start of transcription, the 5' end of the mRNA being synthesized is bound by a cap-synthesizing complex associated with RNA polymerase . (wikipedia.org)
  • After transcription has been terminated, the mRNA chain is cleaved through the action of an endonuclease complex associated with RNA polymerase. (wikidoc.org)
  • Furthermore, in these organisms, RNA polymerase II promoters have not been identified. (pnas.org)
  • RNA was synthesized from linear DNA templates by using the Ampliscribe T7 RNA polymerase kit from Epicentre Technologies (Madison, WI). (pnas.org)
  • These are transcribed by RNA polymerase I . 5S occurs in tandem arrays (~200-300 true 5S genes and many dispersed pseudogenes), the largest one on the chromosome 1q41-42. (wikidoc.org)
  • 5S rRNA is transcribed by RNA polymerase III . (wikidoc.org)
  • RNA vaccines traditionally consist of messenger RNA synthesized by in vitro transcription using a bacteriophage RNA polymerase and template DNA that encodes the antigen(s) of interest. (hindawi.com)
  • The sequence of base pairs is transcribed from DNA by an enzyme called RNA polymerase . (wikipedia.org)
  • De novo synthesis of RNA by the dengue virus RNA-dependent RNA polymerase exhibits temperature dependence at the initiation but not elongation phase. (microbiologyresearch.org)
  • 3D is the RNA-dependent RNA polymerase (RdRP). (wikipedia.org)
  • We have used bacteriophage T7 RNA polymerase (T7RNAP) to study the transcriptional accessibility of ES chromatin in vivo . (embopress.org)
  • The MTAD domain mediates interaction with the RNA polymerase II holoenzyme. (abcam.com)
  • RNAs are the direct products of genes, and these small RNAs can direct enzyme complexes to degrade messenger RNA (mRNA) molecules and thus decrease their activity by preventing translation, via post-transcriptional gene silencing. (wikipedia.org)
  • Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that guide chemical modifications ( methylation or pseudouridylation ) of ribosomal RNAs (rRNAs) and other RNA genes. (wikidoc.org)
  • microRNA (also miRNA) are RNA genes that are the reverse complement of portions of another gene's mRNA transcript and alter the expression of one or several genes through RNA interference . (wikidoc.org)
  • gRNAs (for guide RNA) are RNA genes that function in RNA editing . (wikidoc.org)
  • The Brd family genes also regulate neural development, via the formation of RNA:RNA duplexes with proneural transcripts [ 17 ]. (hindawi.com)
  • Yamamoto, Y 2003, ' Specific RNA interference in psbP genes encoded by a multigene family in Nicotiana tabacum with a short 3'-untranslated sequence ', Bioscience Biotechnology and Biochemistry , vol. 67, pp. 107-113. (elsevier.com)
  • There are a number of RNAs which regulate genes, that is, they regulate the rate at which genes are transcribed or translated. (wikipedia.org)
  • Moreover, 82 genes for untranslated RNAs were identified and annotated. (psu.edu)
  • Incubation of synthetic RNAs corresponding to the 3′ UTRs of Chlamydomonas chloroplast genes atpB and petD with a chloroplast protein extract resulted in the accumulation of stable processing products. (deepdyve.com)
  • To date, no systemic study on RNA editing of plant nuclear genes has been reported. (biomedcentral.com)
  • The results indicate that RNA editing is an essential RNA-based regulatory layer not only for mitochondrial and chloroplast genes but also for nuclear genes. (biomedcentral.com)
  • The function of this nonprotein-coding RNA (or noncoding RNA) is mostly obscure, despite a larger number of noncoding genes than protein-coding genes. (jci.org)
  • Here, transfer RNAs (tRNAs) bind on one end to specific codons (three-base region) in the mRNA and bind on the other end to the amino acids specified by that codon, and thus place the amino acids in the correct sequence in the growing polypeptide according to the template (sequence of nucleotides) provided by the mRNA (Alberts et al. (newworldencyclopedia.org)
  • Transfer RNA ( tRNA ) is a short molecule of about 80 nucleotides which carries a specific amino acid to the polypeptide chain at a ribosome . (wikipedia.org)
  • as well as long noncoding RNAs (lncRNAs) that are longer than 200 nucleotides. (biomedcentral.com)
  • Currently, jViz.RNA employs a unique method for the creation of the RNA molecule layout by mapping the RNA nucleotides into vertexes in a graph, which we call the detailed graph, and then utilizes a Newtonian mechanics inspired system of forces to calculate a layout for the RNA molecule. (biomedcentral.com)
  • RNA is very similar to Deoxyribo-nucleic Acid (DNA) in its basic composition, but while DNA is regularly found as two complimentary strands, RNA can be found as a single strand of nucleotides. (biomedcentral.com)
  • This primary structure (the string of nucleotides) then folds over itself into a secondary structure when the bases in the RNA strands pair up via hydrogen bonding. (biomedcentral.com)
  • lncRNAs represent a burgeoning class of molecules broadly defined as RNA transcripts longer than 200 nucleotides, with no protein-coding potential. (jci.org)
  • Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. (absoluteastronomy.com)
  • Nucleobases are a group of nitrogen-based molecules that are required to form nucleotides, the basic building blocks of DNA and RNA. (absoluteastronomy.com)
  • The sequence of nucleotides allows RNA to encode genetic information. (absoluteastronomy.com)
  • [2] The most common and well-studied example is RNA interference ( RNAi ), in which endogenously expressed microRNA ( miRNA ) or exogenously derived small interfering RNA ( siRNA ) induces the degradation of complementary messenger RNA . (wikipedia.org)
  • Two types of small ribonucleic acid (RNA) molecules - microRNA (miRNA) and small interfering RNA ( siRNA ) - are central to RNA interference. (wikipedia.org)
  • We also looked at the putative host RNA binding protein (RBP) and microRNA binding sites in these regions by 'RBPmap' and 'RNA22 v2' respectively. (bvsalud.org)
  • Although the presence of dsRNA in the cell was previously thought to only occur during viral infection, it is now known that cells express many endogenous small dsRNAs, such as short interfering RNA (siRNAs) and microRNA (miRNAs), which regulate gene expression. (iu.edu)
  • Despite early focus in the literature on RNA interference ( RNAi ) as a core mechanism which occurs at the level of messenger RNA translation, others have since been identified in the broader family of conserved RNA silencing pathways acting at the DNA and chromatin level. (wikipedia.org)
  • Suppression of HuR expression by RNA interference partially blocked the accumulation of ATF3 mRNA following amino acid deprivation. (illinois.edu)
  • Lentiviral delivery of designed shRNAs and the mechanism of RNA interference in mammalian cells. (wikipedia.org)
  • RNA interference ( RNAi ) is a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules. (wikipedia.org)
  • Andrew Fire and Craig C. Mello shared the 2006 Nobel Prize in Physiology or Medicine for their work on RNA interference in the nematode worm Caenorhabditis elegans , which they published in 1998. (wikipedia.org)
  • Moreover, transcription can be inhibited via the pre-transcriptional silencing mechanism of RNA interference, through which an enzyme complex catalyzes DNA methylation at genomic positions complementary to complexed siRNA or miRNA. (wikipedia.org)
  • RNA interference has an important role in defending cells against parasitic nucleotide sequences - viruses and transposons . (wikipedia.org)
  • Double-stranded RNA (dsRNA) recently has been shown to give rise to genetic interference in Caenorhabditis elegans and also is likely to be the basis for phenotypic cosuppression in plants in certain instances. (pnas.org)
  • We developed a multiplex RNA interference technique to downregulate S1P 1 in mice. (jci.org)
  • This is called RNA interference . (wikipedia.org)
  • To investigate the role of SGF14c during soybean nodulation, RNA interference was employed to silence SGF14c expression in soybean roots using Agrobacterium rhizogenes -mediated root transformation. (plantphysiol.org)
  • Due to the paleopolyploid nature of soybean, designing a specific RNA interference sequence that exclusively targeted SGF14c was not possible. (plantphysiol.org)
  • The Dicer enzyme, which generates small RNAs in the miRNA and RNA interference pathways, is essential for meiotic maturation of mouse oocytes. (bio-medicine.org)
  • RNA interference directed against PHD2, but not PHD1 or PHD3, is sufficient to stabilize HIF-1α in normoxia. (biochemj.org)
  • Micro RNAs (miRNA) act by joining an enzyme and blocking mRNA, or speeding its breakdown. (wikipedia.org)
  • The transcripts represented the viral RNA sequence from nt 315 to 1155, its derivatives with internal deletions or truncated forms. (nih.gov)
  • This set of transcripts has allowed us to find out that the factor (p58) binds to EMCV RNA within the sequence 315-485. (nih.gov)
  • [4] CDGS involves the assembly of small RNA complexes on nascent transcripts and is regarded as encompassing mechanisms of action which implicate transcriptional gene silencing (TGS) and co-transcriptional gene silencing (CTGS) events. (wikipedia.org)
  • The sequence and structure of the 3′-untranslated regions of chloroplast transcripts are. (deepdyve.com)
  • The editing events of some nuclear transcripts are highly enriched surrounding the borders between coding sequences (CDSs) and 3′ untranslated regions (UTRs), suggesting site-specific editing. (biomedcentral.com)
  • Furthermore, RNA editing is potentially implicated in new start or stop codon generation, and may affect alternative splicing of certain protein-coding transcripts. (biomedcentral.com)
  • To our knowledge, the results provide the first global view of RNA editing in plant nuclear transcripts. (biomedcentral.com)
  • However, a global vision of RNA editing in plant nuclear protein-coding transcripts has not been realized. (biomedcentral.com)
  • The data presented could serve as a repository for further analyses, and it will lead to a shift of RNA editing research from well-characterized mitochondrial and plastid transcripts to nuclear transcripts in plants. (biomedcentral.com)
  • Design By utilising large scale transcriptome sequencing of three paired HCC clinical specimens and their adjacent non-tumour (NT) tissue counterparts at depth, we discovered an average of 20 007 inferred A to I (adenosine to inosine) RNA editing events in transcripts. (bmj.com)
  • Sequence derived from TEs has also been implicated in both degradation [ 20 ] and increasing the translation [ 21 ] of RNA transcripts. (biomedcentral.com)
  • The current study uncovered the pathogenic role and underlying mechanism of a novel Smad3-dependent long noncoding RNA (lncRNA) (LRNA9884) in type 2 diabetic nephropathy (T2DN). (diabetesjournals.org)
  • X-chromosome inactivation (XCI) in female mammals depends on the noncoding RNA X inactivation specific transcript (Xist). (biomedsearch.com)
  • The long noncoding RNA Morrbid regulates CD8 T cells in response to viral infection. (harvard.edu)
  • One particular subclass, long noncoding RNAs (lncRNAs), represents a large family of noncoding RNA molecules with potentially broad implications for basic science, health, and disease. (jci.org)
  • Long non-coding RNAs (lncRNAs) are increasingly recognized as regulators of tissue-specific cellular functions and have been shown to regulate transcriptional and translational processes, acting as signals, decoys, guides, and scaffolds. (biomedcentral.com)
  • The present study was performed to distinguish non‑coding disease‑causing mutations from neutral ones, and to prioritize potential cancer-associated long non-coding RNAs (lncRNAs) with a logistic regression model in lung cancer. (spandidos-publications.com)
  • The messenger RNA 3'-untranslated region (3'UTR) is emerging as critically important in regulating gene expression at posttranscriptional levels. (nih.gov)
  • RNA silencing describes several mechanistically related pathways which are involved in controlling and regulating gene expression. (wikipedia.org)
  • Using small interfering RNA (siRNA) against MADP1, defective viral RNA synthesis was observed in the knockdown cells, therefore indicating the importance of the protein in coronaviral RNA synthesis. (ntu.edu.sg)
  • Each siRNA is unwound into two single-stranded RNAs (ssRNAs), the passenger strand and the guide strand. (wikipedia.org)
  • This sets them apart from small interfering RNAs (siRNA) which are about the same length, but double-stranded and derived from double-stranded RNA such as dsRNA viruses and small hairpin RNAs (shRNA). (wikidoc.org)
  • The small interfering RNA (siRNA) for S1P 1 specifically silenced the cognate transcript in endothelial cells and inhibited endothelial cell migration in vitro and the growth of neovessels into subcutaneous implants of Matrigel in vivo. (jci.org)
  • The canonical translation initiation pathway begins with cap-dependent attachment of the small ribosomal subunit (SSU) to the messenger ribonucleic acid (mRNA) followed by an energy-dependent, sequential 'scanning' of the 5′ untranslated regions (UTRs). (mdpi.com)
  • Untranslated regions (UTRs) are sections of the mRNA before the start codon and after the stop codon that are not translated, termed the five prime untranslated region (5' UTR) and three prime untranslated region (3' UTR), respectively. (newworldencyclopedia.org)
  • Now, researchers from Hanyang University , Korea have developed heuristic and regression methods to estimate and quantify the usage of 3′ UTRs with widely profiled RNA sequencing (RNA-seq) data. (rna-seqblog.com)
  • With this approach, the 3′ UTR usage estimated from RNA-seq was found to be highly correlated to that of 3P-seq, and poly(A) cleavage signals of 3′ UTRs were detected upstream of the predicted poly(A) cleavage sites. (rna-seqblog.com)
  • In this study, we show that RNAs containing 5' and 3' untranslated regions ( UTRs ) of DTMUV, mosquito -borne Tembusu virus (TMUV) and Japanese encephalitis virus can be translated in a cap-independent manner in mammalian, avian and mosquito cells . (bvsalud.org)
  • Instead, cap-independent translation of DTMUV RNA was dependent on the presence of a 3'UTR , RNA secondary structures located in both UTRs and specific RNA sequences . (bvsalud.org)
  • mRNA untranslated regions - UTRs - are involved in the post‐transcriptional regulation of gene expression by modulating the mRNA stability, nucleocytoplasm transport, subcellular localisation and translation efficiency, thus allowing a fine control of the protein product. (els.net)
  • White boxes represent UTRs (untranslated regions). (rcsb.org)
  • A protein factor that specifically binds to the 5'-untranslated region of encephalomyocarditis virus (EMCV) RNA has been found in extracts of ascites carcinoma Krebs-2 cells. (nih.gov)
  • A 3' untranslated region variant in FMR1 eliminates neuronal activity-dependent translation of FMRP by disrupting binding of the RNA-binding protei. (nih.gov)
  • The gene underlying the disorder, fragile X mental retardation 1 (FMR1), is silenced in most cases by a CGG-repeat expansion mutation in the 5' untranslated region (UTR). (nih.gov)
  • The role of the 3' untranslated region (3'UTR) in the replication of enteroviruses has been studied with a series of mutants derived from either poliovirus type 3 (PV3) or a PV3 replicon containing the reporter gene chloramphenicol acetyltransferase. (asm.org)
  • The RNA-binding domain was mapped to the N-terminal region of MADP1 and the protein binding sequence to stem-loop I of IBV 5'-UTR. (ntu.edu.sg)
  • Multiple copies of potential mRNA destabilizing motifs AUUUA and related sequences can be found to the 3′-untranslated region (UTR) of IL-10 mRNA distributed through three potential regulatory regions. (jimmunol.org)
  • Consistent with this, we observed multiple copies of potential mRNA-destabilizing motifs AUUUA and AU-rich elements (ARE) 3 ( 11 ) in the 3′-untranslated region (UTR) of mouse IL-10 mRNA ( 12 ). (jimmunol.org)
  • The present invention describes the use of hybrid short 3′ untranslated (3′UTR) regions which are composed of two regions, one region from an 3′ untranslated region of a stable eukaryotic mRNA, and another region from the downstream end of an 3′ untranslated region of another eukaryotic mRNA that contains a polyadenylation (polyA) signal. (freepatentsonline.com)
  • Length increase of the human α-globin 3′-untranslated region disrupts stability of the pre-mRNA but not that of the mature mRNA," Journal of Biological Chemistry, 2000, vol. 275, pp. 30248-30255. (freepatentsonline.com)
  • Translational efficiency is regulated by the length of the 3′ untranslated region," Molecular and Cellular Biology, 1996, vol. 16, No. 1, pp. 146-156. (freepatentsonline.com)
  • The 3′ untranslated region (3′ UTR) of mRNA contains elements that play regulatory roles in polyadenylation, localization, translation efficiency, and mRNA stability. (rna-seqblog.com)
  • Phosphorodiamidate morpholino targeting the 5′ untranslated region of the ZIKV RNA inhibits virus replication. (meharryresearch.org)
  • The mRNA for CspA, a major cold shock protein in Escherichia coli , contains an unusually long (159 bases) 5′ untranslated region (5′-UTR), and its stability has been shown to play a major role in cold shock induction of CspA. (asm.org)
  • While constructing a plasmid vector for transfection of trypanosome cells, we serendipitously discovered that in vivo expression of dsRNA of the α-tubulin mRNA 5′ untranslated region (5′ UTR) led to multinucleated cells with striking morphological alterations and a specific block of cytokinesis. (pnas.org)
  • The RNA has a region with double-stranded structure. (google.com)
  • Inhibition is sequence-specific in that the nucleotide sequences of the duplex region of the RNA and of a portion of the target gene are identical. (google.com)
  • In this report, we identified that the TM 5′ untranslated region (UTR) bearing the internal ribosome entry site (IRES) element controls TM protein expression. (elsevier.com)
  • For example, zip-code binding protein 1 (ZBP1, also called IGF-II mRNA binding (IMP1)) protein was shown to bind to a 56 nucleotide (nt) stem-loop structure in the 3′ untranslated region (UTR) of β- actin mRNA ( Actb ), and this binding is necessary for axonal transport of the mRNA ( 6 , 7 ). (mcponline.org)
  • Hughes MJ and Andrews DW (1997) A single nucleotide is a sufficient 5′ untranslated region for translation in an eukaryotic in vitro system. (els.net)
  • While it is established that the 5' region of Xist RNA, comprising the A-repeats and holding 7.5-8.5 copies of a conserved 26-mer sequence, is essential for Xist-mediated silencing, high-resolution structural information for the A-repeats is not available. (biomedsearch.com)
  • The region at the 3' end of a messenger RNA transcript, which is not translated. (sigmaaldrich.com)
  • In vitro mRNA degradation studies demonstrated that the 5'-untranslated region confers increased stability to CYP17 mRNA in PCOS theca cells and showed that the 5'-untranslated region of CYP17 also confers forskolin-stimulated stabilization of CYP17 mRNA. (biomedsearch.com)
  • The 5' untranslated region contains an internal ribosomal entry site (Type I IRES). (wikipedia.org)
  • Other miRNAs are known to promote myogenesis, but only miR669a and miR669q act upstream of myogenic regulatory factors to prevent myogenesis by directly targeting the MyoD 3′ untranslated region. (rupress.org)
  • To date, among the miRNAs known to regulate skeletal myogenesis, only miR669a and miR669q directly inhibit the MyoD 3′ untranslated region (UTR) and, consequently, skeletal myogenesis. (rupress.org)
  • Initially, Affymetrix microarrays were used to detect transcription in this region, Northern blot experiments and mutation analysis were then employed to characterise the RNA transcript. (wikipedia.org)
  • In molecular genetics, the three prime untranslated region (3′-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon. (wikipedia.org)
  • Several regions of the mRNA molecule are not translated into a protein including the 5' cap, 5' untranslated region, 3′ untranslated region and poly(A) tail. (wikipedia.org)
  • Regulatory regions within the 3′-untranslated region can influence polyadenylation, translation efficiency, localization, and stability of the mRNA. (wikipedia.org)
  • Messenger Ribonucleic Acid ( mRNA ) is a molecule of RNA encoding a chemical "blueprint" for a protein product. (wikidoc.org)
  • RNA is an acronym for ribonucleic acid , a nucleic acid . (wikipedia.org)
  • Untranslated regions cover over a third of a typical human mRNA and often contain a range of regulatory elements. (springer.com)
  • In the past few years, the importance of regulation of virulence factors by small regulatory RNA (sRNAs) has been increasingly appreciated. (frontiersin.org)
  • Moreover, while small regulatory RNAs can be relatively easily classified on the basis of their length, secondary structure, and biochemical pathway, the classification of long "mRNA-like" ncRNAs has been problematic. (unimi.it)
  • MiRNAs are a class of short, 20- to 22-nt-long regulatory RNAs expressed in plants and animals 1 , 2 . (pubmedcentralcanada.ca)
  • RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. (nature.com)
  • Within this context, intragenic non-coding RNA cis -regulatory elements (RREs) provide an essential post-transcriptional control layer, through regulation of RNA stability, localisation and processing 1 . (nature.com)
  • Group 1 Innate Lymphoid Cell Lineage Identity Is Determined by a cis-Regulatory Element Marked by a Long Non-coding RNA. (harvard.edu)
  • Regulatory small RNAs (sRNAs) in bacterial genomes have become a focus of research over the past 8 years. (asm.org)
  • Our results, shows for the first time in SARS-Cov-2 infection, a possible cross-talk between host RBPs- miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus . (bvsalud.org)
  • To explore further this possibility, the scientists injected a reporter transcript, a message RNA that is not a normally present in the oocyte but contained sequences that would interact with miRNAs in the oocyte. (bio-medicine.org)
  • RNA silencing may also be defined as sequence-specific regulation of gene expression triggered by double-stranded RNA ( dsRNA ). (wikipedia.org)
  • For example, these studies demonstrated that enzymes detect double-stranded RNA ( dsRNA ) not normally found in cells and digest it into small pieces that are not able to cause disease. (wikipedia.org)
  • The RNAi pathway is found in many eukaryotes , including animals, and is initiated by the enzyme Dicer , which cleaves long double-stranded RNA (dsRNA) molecules into short double-stranded fragments of ~21 nucleotide siRNAs . (wikipedia.org)
  • Exogenous dsRNA initiates RNAi by activating the ribonuclease protein Dicer, [8] which binds and cleaves double-stranded RNAs (dsRNAs) in plants, or short hairpin RNAs (shRNAs) in humans, to produce double-stranded fragments of 20-25 base pairs with a 2-nucleotide overhang at the 3' end. (wikipedia.org)
  • In humans, the most frequent type of editing is the conversion of A to I, which is catalysed by the dsRNA specific ADAR family of RNA editing enzymes. (bmj.com)
  • When transcribed, interaction between two Alus that are in opposite orientation gives rise to double-stranded RNA (dsRNA). (iu.edu)
  • Messenger RNA ( mRNA ) is a large family of RNA molecules that convey genetic information from DNA to the ribosome , where they specify the amino acid sequence of the protein products of gene expression . (wikipedia.org)
  • In eukaryotic organisms most messenger RNA (mRNA) molecules are polyadenylated at the 3' end, but recent studies have shown that short stretches of uridine (oligouridylation) are also common. (wikipedia.org)
  • Another RNA-binding protein, AUF1, regulates target mRNA molecules by enhancing their decay. (illinois.edu)
  • RNAi is an RNA-dependent gene silencing process that is controlled by the RNA-induced silencing complex (RISC) and is initiated by short double-stranded RNA molecules in a cell's cytoplasm, where they interact with the catalytic RISC component argonaute . (wikipedia.org)
  • Splicing is usually performed by an RNA-protein complex called the spliceosome , but some RNA molecules are also capable of catalyzing their own splicing ( see ribozymes ). (wikidoc.org)
  • In eukaryotic organisms, most messenger RNA (mRNA) molecules are polyadenylated at the 3' end. (wikidoc.org)
  • The elucidation of the mechanisms by which these modifications impact cellular processes necessitates the ability to both detect and quantify the presence of these modifications within RNA molecules. (mendeley.com)
  • Small nuclear RNA (snRNA) is a class of small RNA molecules that are found within the nucleus of eukaryotic cells. (wikidoc.org)
  • Small Cajal Body specific RNAs (scaRNAs) are a class of small RNA molecules similar to snoRNAs which specifically localize in the Cajal body , a nuclear organelle involved in the biogenesis of snRNPs . (wikidoc.org)
  • RNA visualization software tools have traditionally presented a static visualization of RNA molecules with limited ability for users to interact with the resulting image once it is complete. (biomedcentral.com)
  • From humans to bacteria and viruses, there are many examples of RNA molecules that are important to understand, classify, and research. (biomedcentral.com)
  • While for small RNA molecules such as transfer RNA (tRNA), this problem almost never arises, for large RNA molecules, this layout can be such that sections of the RNA overlap each other, making annotation of certain regions problematic and uninformative. (biomedcentral.com)
  • Meanwhile, all the untranslated mRNA molecules remain yellow. (healthcanal.com)
  • in particular, BNT162b2 protects the lower respiratory tract against the presence of viral RNA and shows no evidence of disease enhancement. (nature.com)
  • The terminal nts of the viral genomes were identified by sequencing cDNA clones of the plus- and/or minus-strand of the viral double-stranded (ds) RNAs generated using 5′ and 3′ rapid amplification of cDNA ends. (springer.com)
  • acting sequences and secondary structures in untranslated regions of duck Tembusu virus RNA are important for cap-independent translation and viral proliferation. (bvsalud.org)
  • There are four main categories of cancer vaccines: (1) peptide vaccines, (2) cellular vaccines, including tumor cell and immune cell vaccines, (3) viral vector vaccines, and (4) nucleic acid vaccines, including DNA and RNA vaccines. (hindawi.com)
  • The viral protein 2C brings positive sense RNA genomes to the endoplasmic reticulum where assembly and maturation will occur. (wikipedia.org)
  • RNA replication takes place at specialized intracellular membrane structures called 'membranous webs' or 'membrane-associated foci', whereas viral assembly probably occurs on lipid droplets and endoplasmic reticulum. (clinsci.org)
  • Transfer RNA (tRNA), that mediates recognition of the codon and provides the corresponding amino acid, and ribosomal RNA (rRNA), that is the central component of the ribosome's protein-manufacturing machinery. (wikipedia.org)
  • Transfer RNA (tRNA) is RNA that transfers the correct amino acid to a growing polypeptide chain at the ribosomal site of protein biosynthesis during translation. (wikidoc.org)
  • Ribosomal RNA (rRNA) is the primary constituent of ribosomes . (wikidoc.org)
  • They are transfer RNA (tRNA) and ribosomal RNA (rRNA). (wikipedia.org)
  • Ribosomal RNA ( rRNA ) is the catalytic component of the ribosomes. (wikipedia.org)
  • In the cytoplasm, ribosomal RNA and protein combine to form a nucleoprotein called a ribosome. (wikipedia.org)
  • Over the last 10 years, the study of RNA metabolism in trypanosomatid protozoa has unraveled novel mechanisms of eukaryotic gene expression such as polycistronic transcription ( 1 ), trans-splicing ( 2 , 3 ), mitochondrial RNA editing ( 4 - 6 ), and coupling of trans-splicing and polyadenylation ( 7 ). (pnas.org)
  • Notwithstanding our present limited knowledge of these subjects, it appears that trypanosome mRNA abundance is primarily, if not solely, regulated at the level of RNA metabolism rather that at the level of transcription initiation, as is the case in most eukaryotic organisms. (pnas.org)
  • Importantly, both AS isoforms and the identified ecircRNA were significantly dysregulated in peripheral blood mononuclear cells of relapsing-remitting MS patients compared to controls, further supporting the notion that aberrant RNA metabolism is a characteristic feature of the disease. (mdpi.com)
  • Other, less conserved, cis-acting elements and their functional role in different steps of RNA maturation and metabolism will be discussed. (intechopen.com)
  • CspA can bind to single-stranded DNA and RNA without high sequence specificity and has been proposed to function as an RNA chaperone at low temperature ( 16 ). (asm.org)
  • The family Closteroviridae , to which Citrus tristeza virus [CTV] belongs, comprises members with single-stranded (ss)-, positive polarity RNA genomes that are the largest among plant-infecting viruses. (springer.com)
  • They are positive-sense, single-stranded, non-enveloped RNA viruses with icosahedral geometry. (wikipedia.org)
  • Coxsackievirus B4 is one of the six serotypes found in Group B and is a positive sense, single-stranded, non-enveloped RNA virus. (wikipedia.org)
  • For positive sense, single-stranded RNA viruses, translation occurs before transcription. (wikipedia.org)
  • Single stranded, functional RNA is an important agent in many biological processes. (biomedcentral.com)
  • By using high-throughput RNA sequencing, we uncovered the involvement of lncRNAs in renal diseases on both anti- glomerular basement membrane (GBM) and unilateral ureteric obstruction (UUO)-induced mouse kidney disease models and identified 21 novel Smad3-dependent lncRNAs participating in the renal pathogenesis ( 12 ). (diabetesjournals.org)
  • Polyadenylation is the covalent linkage of a polyadenylyl moiety to a messenger RNA molecule. (wikipedia.org)
  • The most well-studied outcome is post-transcriptional gene silencing, which occurs when the guide strand pairs with a complementary sequence in a messenger RNA molecule and induces cleavage by Argonaute 2 (Ago2), the catalytic component of the RISC . (wikipedia.org)
  • A non-coding RNA ( ncRNA ) is any RNA molecule that is not translated into a protein . (wikidoc.org)
  • This is done first by presenting an alternative method for mapping the RNA molecule into a graph, which we call the compressed graph, and then employing advanced numerical integration methods for the compressed graph representation. (biomedcentral.com)
  • The RNA molecule can then twist, fold, or otherwise change its conformation in 3D space, giving it a functional three dimensional form, known as the tertiary structure. (biomedcentral.com)
  • All Visualization software developed for RNA have as their goal to display an informative structure of the RNA molecule, usually focusing on its secondary structure, that can be annotated and used to convey information in presentations, publications, and any other two-dimensional media. (biomedcentral.com)
  • However, the majority of RNA visualization software designed produce a static layout of the RNA molecule that may not be ideal for the user. (biomedcentral.com)
  • Messenger RNA is a molecule of RNA encoding a chemical "blueprint" for a protein product. (absoluteastronomy.com)
  • The DNA sequence from which a non-coding RNA is transcribed as the end product is often called an RNA gene or non-coding RNA gene (see gene ). (wikidoc.org)
  • [1] demonstrating that double-stranded RNA could act as a trigger for gene silencing. (wikipedia.org)
  • [10] These short double-stranded fragments are called small interfering RNAs ( siRNAs ). (wikipedia.org)
  • We have observed that challenging Trypanosoma brucei cells with gene-specific double-stranded RNAs (dsRNAs) leads to specific degradation of the homologous mRNA. (pnas.org)
  • The roles of the double stranded RNA specific ADAR (Adenosine DeAminase that act on RNA) family members (ADARs) and the altered gene specific editing patterns were investigated in clinical specimens, cell models and mice. (bmj.com)
  • Unwinds double-stranded DNA and RNA in a 3' to 5' direction. (abcam.com)
  • Contains 2 DRBM (double-stranded RNA-binding) domains. (abcam.com)
  • The relevance of these observations is discussed in relation to (i) the function of DRs as elements of replication enhancement, (ii) the evolution of RNA secondary structures and (iii) the significance of DRs and secondary structures in MBFV transmissibility between vertebrate and invertebrate hosts. (microbiologyresearch.org)
  • The importance of non-coding RNAs (ncRNAs) in controlling gene expression is becoming increasingly evident. (unimi.it)
  • Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. (plos.org)
  • New discoveries and accelerating progresses in the field of noncoding RNAs (ncRNAs) continuously challenges our deep-rooted doctrines in biology and sometimes our imagination. (mdpi.com)
  • However, in the past two decades, noncoding RNAs (ncRNAs) have garnered increased appreciation for their important roles in regulating various biological processes. (mdpi.com)
  • HuR is an RNA-binding protein that regulates both the stability and cytoplasmic/nuclear localization of mRNA species containing AU-rich elements. (illinois.edu)
  • Several roles in gene expression have been attributed to the untranslated regions, including mRNA stability, mRNA localization, and translational efficiency. (newworldencyclopedia.org)
  • In this review, we will explain why RNA vaccines represent an attractive platform for cancer immunotherapy, discuss modifications to RNA structure that have been developed to optimize mRNA vaccine stability and translational efficiency, and describe strategies for nonviral delivery of mRNA vaccines, highlighting key preclinical and clinical data related to cancer immunotherapy. (hindawi.com)
  • These stem-loops are RNA 3′-end processing signals and determinants of mRNA stability, not transcription terminators. (deepdyve.com)
  • In addition to their characteristic of comparatively higher stability, circRNAs frequently exhibit tissue/developmental stage-specific expression ( 6 , 7 ), and they are thus more suitable as biomarkers than linear RNAs ( 6 , 8 ). (spandidos-publications.com)
  • Posttranscriptional chemical modification of RNA bases is a widespread and physiologically relevant regulator of RNA maturation, stability, and function. (plantcell.org)
  • [2] However, antisense RNA produced intracellularly by an expression vector may be developed and find utility as novel therapeutic agents. (wikipedia.org)
  • Synthetic RNAs of the petA 3′ UTR and the antisense strand of atpB 3′ UTR were degraded in the extract. (deepdyve.com)
  • We distinguish base-pairing sRNAs (antisense RNAs) and sRNAs that act by protein binding (for a review, see reference 5 ). (asm.org)
  • Many trans -encoded antisense RNAs have multiple targets. (asm.org)
  • A range of diverse functions have been proposed for a growing number of characterized small RNA sequences-e.g., regulation of developmental, neuronal cell fate, cell death, proliferation, fat storage, haematopoietic cell fate, insulin secretion. (wikipedia.org)
  • Infection of C2-Idf/C2 heterozygotes with viruses that carry suppressors of RNA silencing relieved the phenotypic inhibition, restoring pigment production and mRNA levels. (genetics.org)
  • RNA is the carrier of genetic information in certain viruses , especially the retroviruses like the HIV virus. (wikipedia.org)
  • [2] rRNA is extremely abundant and makes up 80% of the 10 mg/ml RNA found in a typical eukaryotic cytoplasm . (wikipedia.org)
  • Although the major known function of telomerase in cancer is to replenish telomeric DNA and maintain cell immortality, the regulation of the RNA component of telomerase is not well understood. (isharonline.org)
  • In this review, we discuss several examples of known RNA mechanisms for the regulation of protein synthesis. (isharonline.org)
  • For example, RNA silencing has been shown to be important in the regulation of development and in the control of transposition events. (wikipedia.org)
  • [16] However, the varied and nuanced role of RNA silencing in the regulation of gene expression remains an ongoing scientific inquiry. (wikipedia.org)
  • Hence, the computational RNA-seq method for the estimation of the 3′ UTR landscape would be useful as a tool for studying not only the functional roles of 3′ UTR but also gene regulation by 3′ UTR in a cell type-specific context. (rna-seqblog.com)
  • This is also the case in L. pneumophila where three sRNAs (RsmY, RsmZ, and 6S RNA) were recently shown to be important determinants of virulence regulation and 79 actively transcribed sRNAs were identified. (frontiersin.org)
  • RNA editing is a transcript-based layer of gene regulation. (biomedcentral.com)
  • Finally, we detected small interfering RNAs (siRNAs) in plants carrying C2-Idf , but not in plants homozygous for the wild-type C2 allele. (genetics.org)
  • Mounting evidence has displayed critical roles of circular RNAs (circRNAs) in multiple cancers. (portlandpress.com)
  • Recent evidence suggested that certain circular RNAs (circRNAs) have a crucial role in rheumatic diseases. (spandidos-publications.com)
  • As circRNAs do not have 5′ or 3′ ends, they are able to withstand RNase digestion and are more stable than most linear RNAs ( 5 ). (spandidos-publications.com)
  • At the end, we will also discuss recently unraveled activities of circular RNAs (circRNAs). (mdpi.com)
  • Circular RNAs (circRNAs) have emerged as important regulators in carcinogenesis and metastasis. (medscimonit.com)
  • H19 (H19, Imprinted Maternally Expressed Transcript (Non-Protein Coding)) is an RNA Gene, and is affiliated with the non-coding RNA class. (genecards.org)
  • [8] It has also been observed that the major RNA silencing pathways currently identified have mechanisms of action which may involve both post-transcriptional gene silencing (PTGS) [22] as well as chromatin-dependent gene silencing (CDGS) pathways. (wikipedia.org)
  • 2010) Regulated post‐transcriptional RNA cleavage diversifies the eukaryotic transcriptome. (els.net)
  • In human cancers, aberrant post-transcriptional modifications, such as alternative splicing and RNA editing, may lead to tumour specific transcriptome diversity. (bmj.com)
  • RNA editing is a widespread post-transcriptional process contributing to greater cellular transcriptome diversity in eukaryotes. (bmj.com)
  • Alternatively, dendritic cells can be loaded with either tumor associated antigen mRNA or total tumor RNA and delivered to the host to elicit a specific immune response. (hindawi.com)
  • The product of this gene is a long non-coding RNA which functions as a tumor suppressor. (genecards.org)
  • 4. The recombinant nucleic acid of claim 1, wherein the nucleic acid is DNA, RNA, or PNA. (freepatentsonline.com)
  • This review will begin with a brief overview of nucleic acid vaccines for context and will then focus on RNA cancer vaccines. (hindawi.com)
  • By definition, nucleic acid vaccines are vaccines containing antigens encoded by either DNA or RNA. (hindawi.com)
  • [26] RNA silencing refers to the silencing activity of a range of small RNAs and is generally regarded as a broader category than RNAi. (wikipedia.org)
  • While the terms have sometimes been used interchangeably in the literature, RNAi is generally regarded as a branch of RNA silencing. (wikipedia.org)
  • Transcription is when RNA is made from DNA. (wikipedia.org)
  • A 5' cap (also termed an RNA cap, an RNA 7-methylguanosine cap, or an RNA m 7 G cap) is a modified guanine nucleotide that has been added to the "front" or 5' end of a eukaryotic messenger RNA shortly after the start of transcription. (wikipedia.org)
  • Polyadenylation occurs during and/or immediately after transcription of DNA into RNA. (wikipedia.org)
  • Messenger RNA is synthesized on a DNA template in a process known as DNA transcription . (newworldencyclopedia.org)
  • RNA generated from DNA templates by a highly productive, cell-free in vitro transcription process is molecularly well-defined and free of materials of animal origin. (nature.com)
  • We found that c2 transcription occurs in nuclei of C2-Idf/C2 heterozygotes, but mRNA does not accumulate, suggesting that the inhibition is mediated by RNA silencing. (genetics.org)
  • Retrotransposons copy themselves in two stages: first from DNA to RNA by transcription , then from RNA back to DNA by reverse transcription . (wikipedia.org)
  • RatA controls the toxin TxpA ( 39 ), SR1 controls the transcription activator AhrC ( 17 ) (see below), FsrA regulates sdhCAB , citB , yvfW , and leuCD ( 11 ), and BsrA and BsrB are two 6S RNAs ( 1 ). (asm.org)
  • The positive strand RNA genomes of flaviviruses are commonly translated in a cap-dependent manner. (bvsalud.org)
  • It is now evident that nonprotein coding RNA (ncRNA) plays a critical role in regulating the timing and rate of protein translation. (isharonline.org)
  • The in-depth characterization of GSDMB AS and backsplicing profiles led us to the identification of an exonic circular RNA (ecircRNA) as well as of novel GSDMB in-frame and out-of-frame isoforms. (mdpi.com)
  • Circular RNA (circRNA) is a unique type of RNA, which is composed of exons, introns or products of reverse splicing of the two ( 4 ). (spandidos-publications.com)
  • Immunoprecipitation of HuR-RNA complexes followed by reverse transcriptase-PCR analysis showed that HuR interacted with ATF3 mRNA in vivo and that this interaction increased following amino acid limitation. (illinois.edu)
  • Nucleobases provide the molecular structure necessary for the hydrogen bonding of complementary DNA and RNA strands, and are key components in the formation of stable. (absoluteastronomy.com)
  • Scanning through the 5′UTR requires the adenosine triphosphate (ATP)-dependent RNA helicase eukaryotic initiation factor (eIF) 4A and its efficiency contributes to the specific rate of protein synthesis. (mdpi.com)
  • RNA modifications impact numerous cellular processes such as pre-mRNA splicing and protein synthesis. (mendeley.com)
  • This antibiotic is a bacteriostatic agent that inhibits protein synthesis by binding to the 23S RNA of the 50S subunit of bacterial ribosomes. (sigmaaldrich.com)
  • Here, we apply our high-throughput annotation of modified ribonucleotides ( HAMR ) pipeline to identify and classify modifications that affect Watson-Crick base pairing at three different levels of the Arabidopsis thaliana transcriptome (polyadenylated, small, and degrading RNAs). (plantcell.org)
  • Some of the elements contained in untranslated regions form a characteristic secondary structure when transcribed into RNA. (newworldencyclopedia.org)
  • The work presented here focuses on improvements to jViz.RNA that allow the drawing of RNA secondary structures according to common drawing conventions, as well as dramatic run-time performance improvements. (biomedcentral.com)
  • These improvements produce more stable as well as visually aesthetic representations of the RNA secondary structures. (biomedcentral.com)
  • It has been reported that non-coding RNAs regulate the initiation and development of GC. (springer.com)
  • rRNA is transcribed from DNA, like all RNA. (wikidoc.org)
  • long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. (rna-seqblog.com)
  • RNA Synthesis and Transfection. (pnas.org)
  • DNA contains two intercoiled strands, but RNA only contains one single strand. (wikipedia.org)
  • A previously used synonym, particularly with bacteria , was small RNA ( sRNA ). (wikidoc.org)