RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)RNA, Small Interfering: Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.RNA Editing: A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.DNA-Directed RNA Polymerases: Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).RNA Viruses: Viruses whose genetic material is RNA.RNA Interference: A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.RNA, Double-Stranded: RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.RNA, Catalytic: RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.RNA Folding: The processes of RNA tertiary structure formation.RNA Polymerase II: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 220.127.116.11.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.RNA Stability: The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.RNA Helicases: A family of proteins that promote unwinding of RNA during splicing and translation.RNA, Antisense: RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.RNA Processing, Post-Transcriptional: Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.RNA, Transfer: The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.RNA, Small Nuclear: Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.RNA Precursors: RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.RNA, Untranslated: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.RNA Caps: Nucleic acid structures found on the 5' end of eukaryotic cellular and viral messenger RNA and some heterogeneous nuclear RNAs. These structures, which are positively charged, protect the above specified RNAs at their termini against attack by phosphatases and other nucleases and promote mRNA function at the level of initiation of translation. Analogs of the RNA caps (RNA CAP ANALOGS), which lack the positive charge, inhibit the initiation of protein synthesis.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.RNA, Protozoan: Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.RNA, Neoplasm: RNA present in neoplastic tissue.RNA Ligase (ATP): 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 18.104.22.168.DEAD-box RNA Helicases: A large family of RNA helicases that share a common protein motif with the single letter amino acid sequence D-E-A-D (Asp-Glu-Ala-Asp). In addition to RNA helicase activity, members of the DEAD-box family participate in other aspects of RNA metabolism and regulation of RNA function.RNA Polymerase III: 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 22.214.171.124.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.RNA Polymerase I: 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 126.96.36.199.RNA, Nuclear: RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.RNA, Guide: Small kinetoplastid mitochondrial RNA that plays a major role in RNA EDITING. These molecules form perfect hybrids with edited mRNA sequences and possess nucleotide sequences at their 5'-ends that are complementary to the sequences of the mRNA's immediately downstream of the pre-edited regions.RNA, Ribosomal, 28S: Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.RNA, Ribosomal, 23S: Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.RNA Transport: The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.RNA, Spliced Leader: 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).RNA, Satellite: 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)RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.RNA, Archaeal: Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.Nucleic Acid Hybridization: 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)Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Virus Replication: The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.RNA Cleavage: 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.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Oligoribonucleotides: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.RNA, Heterogeneous Nuclear: Nuclear nonribosomal RNA larger than about 1000 nucleotides, the mass of which is rapidly synthesized and degraded within the cell nucleus. Some heterogeneous nuclear RNA may be a precursor to mRNA. However, the great bulk of total hnRNA hybridizes with nuclear DNA rather than with mRNA.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.RNA, Small Cytoplasmic: Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).RNA 3' End Processing: 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.Templates, Genetic: 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.RNA, Small Untranslated: Short RNA, about 200 base pairs in length or shorter, that does not code for protein.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Ribonucleoproteins: Complexes of RNA-binding proteins with ribonucleic acids (RNA).Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.Poly A: A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.RNA, Ribosomal, 5.8S: Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).RNA, Long Noncoding: 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.RNA, Small Nucleolar: 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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.RNA Virus InfectionsProtein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.RNA, Complementary: 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)UridinePromoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Endoribonucleases: 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.-.Cell Nucleus: 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)RNA, Chloroplast: Ribonucleic acid in chloroplasts having regulatory and catalytic roles as well as involvement in protein synthesis.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Kinetics: The rate dynamics in chemical or physical systems.Single-Strand Specific DNA and RNA Endonucleases: 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.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.RNA, Helminth: Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.Plant Viruses: Viruses parasitic on plants higher than bacteria.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.RNA, Transfer, Phe: A transfer RNA which is specific for carrying phenylalanine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Lys: A transfer RNA which is specific for carrying lysine to sites on the ribosomes in preparation for protein synthesis.Ribosomes: Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Oligonucleotides: 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)Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.5' Untranslated Regions: The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.RNA, Transfer, Tyr: A transfer RNA which is specific for carrying tyrosine to sites on the ribosomes in preparation for protein synthesis.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Amanitins: Cyclic peptides extracted from carpophores of various mushroom species. They are potent inhibitors of RNA polymerases in most eukaryotic species, blocking the production of mRNA and protein synthesis. These peptides are important in the study of transcription. Alpha-amanitin is the main toxin from the species Amanitia phalloides, poisonous if ingested by humans or animals.Genes, Viral: The functional hereditary units of VIRUSES.Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.Ribonuclease T1: An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 188.8.131.52.Molecular Weight: The sum of the weight of all the atoms in a molecule.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Cell Nucleolus: Within most types of eukaryotic CELL NUCLEUS, a distinct region, not delimited by a membrane, in which some species of rRNA (RNA, RIBOSOMAL) are synthesized and assembled into ribonucleoprotein subunits of ribosomes. In the nucleolus rRNA is transcribed from a nucleolar organizer, i.e., a group of tandemly repeated chromosomal genes which encode rRNA and which are transcribed by RNA polymerase I. (Singleton & Sainsbury, Dictionary of Microbiology & Molecular Biology, 2d ed)HIV-1: The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.Cell-Free System: 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)Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Genes: 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.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Viral Nonstructural Proteins: 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.RNA, Transfer, Amino Acyl: Intermediates in protein biosynthesis. The compounds are formed from amino acids, ATP and transfer RNA, a reaction catalyzed by aminoacyl tRNA synthetase. They are key compounds in the genetic translation process.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.RNA Splice Sites: 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.RNA, Transfer, Ala: A transfer RNA which is specific for carrying alanine to sites on the ribosomes in preparation for protein synthesis.Poliovirus: 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.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Tobacco: A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.Ribonuclease P: An RNA-containing enzyme that plays an essential role in tRNA processing by catalyzing the endonucleolytic cleavage of TRANSFER RNA precursors. It removes the extra 5'-nucleotides from tRNA precursors to generate mature tRNA molecules.Centrifugation, Density Gradient: Separation of particles according to density by employing a gradient of varying densities. At equilibrium each particle settles in the gradient at a point equal to its density. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Cytoplasm: The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)Nucleotides: The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)Mosaic Viruses: Viruses which produce a mottled appearance of the leaves of plants.RNA-Directed DNA Polymerase: An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC 184.108.40.206.Dactinomycin: A compound composed of a two CYCLIC PEPTIDES attached to a phenoxazine that is derived from STREPTOMYCES parvullus. It binds to DNA and inhibits RNA synthesis (transcription), with chain elongation more sensitive than initiation, termination, or release. As a result of impaired mRNA production, protein synthesis also declines after dactinomycin therapy. (From AMA Drug Evaluations Annual, 1993, p2015)Open Reading Frames: 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).Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Hepacivirus: A genus of FLAVIVIRIDAE causing parenterally-transmitted HEPATITIS C which is associated with transfusions and drug abuse. Hepatitis C virus is the type species.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.RNA, Transfer, Asp: A transfer RNA which is specific for carrying aspartic acid to sites on the ribosomes in preparation for protein synthesis.TritiumRNA, Transfer, Met: A transfer RNA which is specific for carrying methionine to sites on the ribosomes. During initiation of protein synthesis, tRNA(f)Met in prokaryotic cells and tRNA(i)Met in eukaryotic cells binds to the start codon (CODON, INITIATOR).Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Bromovirus: A genus of tripartite plant viruses in the family BROMOVIRIDAE. Transmission is by beetles. Brome mosaic virus is the type species.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Ribonuclease H: A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Regulatory Sequences, Ribonucleic Acid: Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.Polyribosomes: A multiribosomal structure representing a linear array of RIBOSOMES held together by messenger RNA; (RNA, MESSENGER); They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Cell Line, Tumor: A cell line derived from cultured tumor cells.Capsid: The outer protein protective shell of a virus, which protects the viral nucleic acid.Exoribonucleases: A family of enzymes that catalyze the exonucleolytic cleavage of RNA. It includes EC 3.1.13.-, EC 3.1.14.-, EC 3.1.15.-, and EC 3.1.16.-. EC 3.1.-Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Bacterial Proteins: Proteins found in any species of bacterium.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.RNA, Transfer, Gly: A transfer RNA which is specific for carrying glycine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, His: A transfer RNA which is specific for carrying histidine to sites on the ribosomes in preparation for protein synthesis.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.RNA, Transfer, Val: A transfer RNA which is specific for carrying valine to sites on the ribosomes in preparation for protein synthesis.Poly U: A group of uridine ribonucleotides in which the phosphate residues of each uridine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Nodaviridae: A family of RNA viruses infecting insects and fish. There are two genera: Alphanodavirus and Betanodavirus.Nucleic Acid Precursors: Use for nucleic acid precursors in general or for which there is no specific heading.Virus Assembly: The assembly of VIRAL STRUCTURAL PROTEINS and nucleic acid (VIRAL DNA or VIRAL RNA) to form a VIRUS PARTICLE.Defective Viruses: Viruses which lack a complete genome so that they cannot completely replicate or cannot form a protein coat. Some are host-dependent defectives, meaning they can replicate only in cell systems which provide the particular genetic function which they lack. Others, called SATELLITE VIRUSES, are able to replicate only when their genetic defect is complemented by a helper virus.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.RNA, Transfer, Arg: A transfer RNA which is specific for carrying arginine to sites on the ribosomes in preparation for protein synthesis.RNA, Algal: Ribonucleic acid in algae having regulatory and catalytic roles as well as involvement in protein synthesis.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Heterogeneous-Nuclear Ribonucleoproteins: A family of ribonucleoproteins that were originally found as proteins bound to nascent RNA transcripts in the form of ribonucleoprotein particles. Although considered ribonucleoproteins they are primarily classified by their protein component. They are involved in a variety of processes such as packaging of RNA and RNA TRANSPORT within the nucleus. A subset of heterogeneous-nuclear ribonucleoproteins are involved in additional functions such as nucleocytoplasmic transport (ACTIVE TRANSPORT, CELL NUCLEUS) of RNA and mRNA stability in the CYTOPLASM.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Species Specificity: 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.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.Virion: The infective system of a virus, composed of the viral genome, a protein core, and a protein coat called a capsid, which may be naked or enclosed in a lipoprotein envelope called the peplos.Ribonucleoproteins, Small Nuclear: Highly conserved nuclear RNA-protein complexes that function in RNA processing in the nucleus, including pre-mRNA splicing and pre-mRNA 3'-end processing in the nucleoplasm, and pre-rRNA processing in the nucleolus (see RIBONUCLEOPROTEINS, SMALL NUCLEOLAR).Hepatitis Delta Virus: A defective virus, containing particles of RNA nucleoprotein in virion-like form, present in patients with acute hepatitis B and chronic hepatitis. It requires the presence of a hepadnavirus for full replication. This is the lone species in the genus Deltavirus.Ribosomal Proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.RNA, Transfer, Trp: A transfer RNA which is specific for carrying tryptophan to sites on the ribosomes in preparation for protein synthesis.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Terminator Regions, Genetic: DNA sequences recognized as signals to end GENETIC TRANSCRIPTION.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Levivirus: A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.PolynucleotidesTrypanosoma brucei brucei: A hemoflagellate subspecies of parasitic protozoa that causes nagana in domestic and game animals in Africa. It apparently does not infect humans. It is transmitted by bites of tsetse flies (Glossina).DNA Restriction Enzymes: 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.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Tombusvirus: A genus of plant viruses that infects ANGIOSPERMS. Transmission occurs mechanically and through soil, with one species transmitted via a fungal vector. The type species is Tomato bushy stunt virus.Guanosine: A purine nucleoside that has guanine linked by its N9 nitrogen to the C1 carbon of ribose. It is a component of ribonucleic acid and its nucleotides play important roles in metabolism. (From Dorland, 28th ed)Polyadenylation: The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) adds 60-200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here.RNA, Transfer, Leu: A transfer RNA which is specific for carrying leucine to sites on the ribosomes in preparation for protein synthesis.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
RNA editing is the insertion, deletion, and substitution of nucleotides in a mRNA transcript prior to translation to protein. ... These proteins consist of 35-mer repeated amino acids, the sequence of which determines the cis binding site for the edited ... Parasitic plants such as Epifagus virginiana show a loss of RNA editing resulting in a loss of function for photosynthesis ... Tillich, Michael; Krause, Kirsten (2010-07-31). "The ins and outs of editing and splicing of plastid RNAs: lessons from ...
Harold Smith (scientist)
In 2008, he edited a book for Wiley and Sons on RNA and DNA Editing that brought together the next generation of scientists ... "RNA Editing". Gordon Research Conferences. Retrieved 1 June 2014. L Chan (22 May 1994). "Apolipoprotein B Messenger RNA editing ... "The APOBEC1 Paradigm for Mammilian Cytidine Deaminases that Edit DNA and RNA." DNA and RNA Modifications Enzymes: Structure, ... Smith, Harold C. "RNA Editing" Encyclopedia of Life Sciences. : Macmillan Reference Ltd, Stockton Press, 2000. Smith, H.C. ...
"Specificity of ADAR-mediated RNA editing in newly identified targets". Rna. 14 (6): 1110-8. doi:10.1261/rna.923308. PMC 2390793 ... UTR but ADAR2 edits 5b and 5c sites.Y/c is edited by both and edits the Q/R and K/R sites at higher levels than ADAR1. Low ... A to I RNA editing is catalyzed by a family of adenosine deaminases acting on RNA (ADARs) that specifically recognize ... The region that base pairs with the editing region is known as an Editing Complementary Sequence (ECS). The editing sites are ...
... known to be edited. Different levels of editing result in a variety of effects on receptor function. The type of RNA editing ... Editing also occurs in the mouse. The initial demonstration of RNA editing in rat. The predominant isoform in rat brain is VNV ... Therefore, editing can also alter protein function. A to I editing occurs in a non coding RNA sequences such as introns, ... A to I RNA editing is catalyzed by a family of adenosine deaminases acting on RNA (ADARs) that specifically recognize ...
... factor 1 There is some evidence for RNA editing of human WT1 mRNA.As with alternative splicing of the gene RNA editing ... has been shown to decrease repressive regulation of transcription of growth promoting genes in vitro compared to the non edited ... editing is unknown as is the enzyme responsible for this editing.The region where editing occurs like that of other editing ... RNA editing results in an alternative amino acid being translated. The changes in amino acid occur in a region identified as a ...
The pre-mRNA of this protein is subject to RNA editing. A to I RNA editing is catalyzed by a family of adenosine deaminases ... An edited channel passes more current and has a shorter action potential than the non-edited type due to the inability of the ... A stem loop hairpin structure mediates the RNA editing. ADAR2 is likely to be the preferred editing enzyme at the I/V site. ... RNA editing at this position occurs at a highly conserved ion conducting pore of the channel. This may affect the channels role ...
... continue to undergo editing as mature mRNA. A third candidate editing site did not show evidence of RNA editing in sequence ... Editing at the K/R site at amino acid position 95 is very high in the human brain. The edited sites are found within the ... "Screening of human SNP database identifies recoding sites of A-to-I RNA editing". RNA. 14 (10): 2074-85. doi:10.1261/rna.816908 ... The two editing sites were previously recorded as single nucleotide polymorphisms in dbSNP. A to I RNA editing is catalyzed by ...
This indicates that the T/A site may still be shown to be a site of A to I RNA editing. Editing at this site would result in an ... It was only detected in one genomic sample indicating that the edited residue may be an SNP. However, the secondary structure ... The region that pairs with the editing region is known as an Editing Complementary Sequence (ECS). The candidate editing sites ... DARNED (DAtabase of RNa EDiting in humans) Human C1QL1 genome location and C1QL1 gene details page in the UCSC Genome Browser. ...
"The neurofibromatosis type I messenger RNA undergoes base-modification RNA editing". Nucleic Acids Research. 24 (3): 478-485. ... This deamination changes an arginine codon (CGA) to an in-frame translation stop codon (UGA). If the edited transcript is ... The editing site in NF1 mRNA was shown to have high homology to the ApoB editing site, where double stranded mRNA undergoes ... NF1 mRNA editing was believed to involve the ApoB holoenzyme due to the high homology between the two editing sites, however ...
RNA editing. Octopuses and other coleoid cephalopods are capable of greater RNA editing (which involves changes to the nucleic ... This page was last edited on 14 December 2017, at 12:34. ... High levels of RNA editing do not appear to be present in more ... Coleoids rely mostly on ADAR enzymes for RNA editing, which requires large double-stranded RNA structures to flank to the ... More than 60% of RNA transcripts for coleoid brains are recoded by editing, compared to less than 1% for a human or fruit fly. ...
RNA editing. The mRNA transcripts of the SDHB gene in human are edited through an unknown mechanism at ORF nucleotide ... "Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes". PeerJ. 1: e152. doi:10.7717/peerj.152. PMC ... "Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes". PeerJ. 1: e152. doi:10.7717/peerj.152. PMC ... References. *^ a b c GRCh38: Ensembl release 89: ENSG00000117118 - Ensembl, May 2017 ...
RNA editing. The pre-mRNA of this protein is subject to RNA editing. ... Type. A to I RNA editing is catalyzed by a family of adenosine deaminases acting on RNA (ADARs) that specifically ... GABRA3 - a channel subunit which undergoes similar RNA editing. References. *^ a b c GRCh38: Ensembl release 89: ... Consequences. Structure. Editing results in a codon (I/V) change from (ATT) to (GTT) resulting in translation of a ...
RNA editing in plastidsEdit. RNA editing is the insertion, deletion, and substitution of nucleotides in a mRNA transcript prior ... DNA replicationEdit. Leading model of cpDNA replicationEdit. Chloroplast DNA replication via multiple D loop mechanisms. ... Protein synthesisEdit. See also: Transcription and translation. Protein synthesis within chloroplasts relies on an RNA ... Takenaka M, Zehrmann A, Verbitskiy D, Härtel B, Brennicke A (2013). "RNA editing in plants and its evolution". Annual Review of ...
Evolution of biological complexity
1993). "On the evolution of RNA editing". Trends in Genetics. 9 (8): 265-268. doi:10.1016/0168-9525(93)90011-6.. ... References. *^ Werner, Andreas; Piatek, Monica J.; Mattick, John S. (April 2015). "Transpositional shuffling and quality ... RNA editing may have arisen in Trypanosoma brucei. ... Types of trends in complexity. Passive versus active trends in complexity. Organisms at the beginning are red. Numbers ...
Rotamer tools (auto fit rotamer, manual rotamer, mutate and autofit, simple mutate) Torsion editing (edit chi angles, edit main ... Ideal DNA/RNA - build an ideal DNA or RNA fragment. Find ligands - find and fit a model to any small molecule which may be ... Pukka puckers - check for unusual DNA/RNA conformations. Coot is built upon a number of libraries. Crystallographic tools ...
... and its pre-mRNA is subject to RNA editing. A to I RNA editing is catalyzed by a family of adenosine deaminases acting on RNA ( ... In humans, 80-90% of GRIA3 transcripts are edited. The absence of the Q/R site editing in this glutamate receptor subunit is ... Editing results in the targeted adenosine, which is mismatched prior to editing in the double-stranded RNA structure to become ... Editing results in a codon change from (AGA) to (GGA), an R to a G change at the editing site. Editing at R/G site allows for ...
February 2013). "MicroRNA-182-5p targets a network of genes involved in DNA repair". RNA. 19 (2): 230-42. doi:10.1261/rna. ... With the help of CRISPR-Cas9,parts of a genome can be edited by scientists by removing or adding or altering parts in a DNA ... "CRISPR gene-editing tool has scientists thrilled - but nervous" CBC news. Author Kelly Crowe. November 30, 2015. Listen to this ... Unlike proteins and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level ...
The agents that are competent to edit genetic codes are viruses or subviral RNA-agents. Although GEEN has higher efficiency ... named genome editing as a potential weapon of mass destruction, stating that genome editing conducted by countries with ... Genome editing was selected by Nature Methods as the 2011 Method of the Year. The CRISPR-Cas system was selected by Science as ... Baker, M., Gene-editing nucleases. Nat Meth 9 (1), 23-26 (2012). Rebar, EJ; Huang, Y; Hickey, R; Nath, AK; Meoli, D; Nath, S; ...
The edited residue was previously recorded as a single nucleotide polymorphism(SNP) in dbSNP. A to I RNA editing is catalyzed ... "Specificity of ADAR-mediated RNA editing in newly identified targets". RNA. 14 (6): 1110-8. doi:10.1261/rna.923308. PMC 2390793 ... The region that base pairs with the editing region is known as an Editing Complentary Sequence (ECS). The one editing site of ... Editing at the Q/R site is likely to involve both ADAR1 and ADAR2.Mice ADAR2 knockouts show a decrease in editing at the Q/R ...
RNA editing - Wikipedia
Editing events may include the insertion, deletion, and base substitution of nucleotides within the edited RNA molecule. RNA ... RNA editing website DARNED (DAtabase of RNa EDiting in humans) A-to-I editing website C-to-U Editing Website. ... A-to-I editing is the main form of RNA editing in mammals and occurs in regions of double-stranded RNA (dsRNA). Adenosine ... Therefore, a RNA transcript requiring extensive editing will need more than one guide RNA and editosome complex. The editing ...
Highly efficient RNA-guided base editing in rabbit | Nature Communications
... strategy can be used to precisely mimic human pathologies by efficiently inducing nonsense or missense mutations as well as RNA ... b-f Representative sequencing chromatograms at Dmd, Otc-1, Otc-2, Sod1-1, and Sod1-2 targets of WT and edited rabbit ... Highly efficient RNA-guided base editing in rabbit. *Zhiquan Liu1. na1, ... 1a). Base editing was conducted in rabbit zygotes by microinjection of BE3-encoding mRNA and single guide RNAs (sgRNAs). Sanger ...
RNA editing implicated in chloroplast-to-nucleus communication | PNAS
... an essential chloroplast protein and a core component of the RNA editosome that edits many of the RNAs that are edited in ... RNA editing has been reported in viruses and diverse eukaryotes. In flowering plants, RNA editing converts cytidines to ... They report that in norflurazon-treated seedlings, RNA editing is altered at 21 sites and that GUN1 affects RNA editing at 11 ... In these cells, GUN1 accumulates and regulates RNA editing by interacting with MORF2 (red arrow). Abnormal RNA editing ...
RCas9: A programmable RNA editing tool | EurekAlert! Science News
A powerful scientific tool for editing the DNA instructions in a genome can now also be applied to RNA as Berkeley Lab ... researchers have demonstrated a means by which the CRISPR/Cas9 protein complex can be programmed to recognize and cleave RNA at ... Together, CRISPR and Cas9 can be used to precisely edit the DNA instructions in a targeted genome for making desired types of ... RCas9: A programmable RNA editing tool. DOE/Lawrence Berkeley National Laboratory. Journal. Nature. Funder. National Institutes ...
Largest, most accurate list of RNA editing sites | EurekAlert! Science News
The list yielded several biological insights and can aid further research on RNA transcription because flies are a common model ... Researchers have compiled the largest and most rigorously validated list to date of the genetic sites in fruit flies where RNA ... transcribed from DNA is then edited by an enzyme to affect a wide variety of fundamental biological functions. ... IMAGE: The two two dark humps in the top row (representing fly RNA) are missing in flies that lack the enzyme to edit RNA ( ...
Squid Enrich Their DNA "Blueprint" Through Prolific RNA Editing
By comparing DNA and RNA sequences from the squid brain, the team found that 60 percent of the RNA transcripts had been edited ... RNA editing was thought to be sparingly used, based on a limited number of studies in mammals and flies. But recently, MBL ... "In squid, RNA editing is so pervasive that the central dogma should be modified to include this process," Rosenthal says. " ... Alon S et al (2015) The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing. ...
A-to-I RNA editing - immune protector and transcriptome diversifier | Nature Reviews Genetics
The most common type of RNA editing is A-to-I editing by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. ... RNA editing is unique among these modifications because it not only alters the cellular fate of RNA molecules but also alters ... Editing of these non-coding sites is thought to have a critical role in protecting against activation of innate immunity by ... The results have changed our understanding of the extent and distribution of A-to-I editing and its role in evolution and ...
Identification of widespread ultra-edited human RNAs
A-to-I RNA editing) is an important mechanism that increases transciptome diversity. It occurs when a genomically encoded ... Adenosine-to-inosine modification of RNA molecules (A-to-I RNA editing) is an important mechanism that increases transciptome ... However, such methods perform poorly on RNAs that underwent extensive editing ("ultra"-editing), as the large number of ... Identification of widespread ultra-edited human RNAs PLoS Genet. 2011 Oct;7(10):e1002317. doi: 10.1371/journal.pgen.1002317. ...
CRISPR-Cas Base Editing Technology Can Cause Transcriptome-Wide RNA Off-Target Edits | GenomeWeb
Researchers found that both CBEs and ABEs can cause transcriptome-wide RNA edits, which has implications for the research and ... CRISPR-Cas Base Editing Technology Can Cause Transcriptome-Wide RNA Off-Target Edits. Apr 17, 2019 ... Home » CRISPR-Cas Base Editing Technology Can Cause Transcriptome-Wide RNA Off-Target Edits ... Joung has reported in a new study that CRISPR-Cas base editing technology can induce transcriptome-wide off-target RNA editing ...
GUN1 interacts with MORF2 to regulate plastid RNA editing during retrograde signaling | PNAS
The rpoB-338 site was not edited in the ys1 mutant (SI Appendix, Fig. S10), while its editing level was down-regulated in gun1 ... NF treatment also affected RNA editing in plastids (16, 17). RNA editing is a posttranscriptional modification of RNA that ... In this study, we have discovered an unexpected role for GUN1 in plastid RNA editing, as gun1 mutations affect RNA-editing ... GUN1 plays a direct role in RNA editing by physically interacting with MULTIPLE ORGANELLAR RNA EDITING FACTOR 2 (MORF2). MORF2 ...
CRISPR-based method allows for reversible RNA editing | FierceBiotech
Broad Institute scientists have created a CRISPR-based method that targets RNA in a way that makes reversible changes to DNA ... CRISPR-Cas9 gene editing has been useful for blocking specific genes to correct mutations, but it makes permanent changes to ... RNA Editing for Programmable A to I Replacement) can edit single nucleosides, or the "letters" that make up the RNA helix. ... causing the RNA to clump together in cells. The RNA-targeted CRISPR managed to clear the majority of clumps and errant RNA ...
CRISPR base editors can induce wide-ranging off-target RNA edits - Massachusetts General Hospital, Boston, MA
... can induce widespread off-target effects in RNA, extending beyond the targeted DNA. ... Our goal is to generate a suite of base editors with minimized RNA editing activities that can be used for both research and ... "We were also glad to see that we could substantially reduce those unwanted RNA edits with our SECURE base editor variants." ... "We were quite surprised at the number - tens of thousands - of RNA edits and the frequency of these alterations that we ...
Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors
CBE-induced RNA edits occur in both protein-coding and non-protein-coding sequences and generate missense, nonsense, splice ... Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. - PubMed - NCBI. Abstract. CRISPR-Cas base ... These variants also showed more precise on-target DNA editing than the wild-type CBE and, for most guide RNAs tested, no ... Finally, we show that an adenine base editor7 can also induce transcriptome-wide RNA edits. These results have implications for ...
New CRISPR platform expands RNA editing capabilities | Science Codex
RESCUE can be guided to any RNA of choice, then perform a C-to-U edit through the evolved ADAR2 component of the platform. The ... Expanding the reach of RNA editing to new targets. The previously developed REPAIR platform used the RNA-targeting CRISPR/Cas13 ... A major advantage of RNA editing is its reversibility, in contrast to changes made at the DNA level, which are permanent. Thus ... In addition, some cell types, such as neurons, are difficult to edit using CRISPR/Cas9-mediated editing, and new strategies are ...
A way to minimize unexpected base edits to cellular RNA
... with the Broad Institute of Harvard and MIT has found evidence showing that using base editors can lead to unexpected RNA ... cellular edits. In their paper published in the journal Science Advances, the ... ... The researchers conclude by noting that because of low levels of RNA editing and the short half-life of RNA, the degree of ... that retained their ability to make the desired base edits but caused less RNA editing. They further report that the new ...
Edited RNA + invasive DNA add individuality - Healthcanal.com : Healthcanal.com
Editing of double-stranded RNA - or a lack of editing - has already been linked to diseases in people, including amyloid ... which edits RNA in humans, flies, and many other creatures, edits double-stranded RNAs. This loosens the system that keeps " ... They identified specific editing sites and signs of editing on the double stranded RNA. ... A study in Nature Communications finds that an enzyme that edits RNA may loosen the genomes control over invasive snippets of ...
Frontiers | Uncovering RNA Editing Sites in Long Non-Coding RNAs | Bioengineering and Biotechnology
... based on RNA-seq experiments, have clearly demonstrated that a large fraction of RNA editing events alter non-coding RNAs ... based on RNA-seq experiments, have clearly demonstrated that a large fraction of RNA editing events alter non-coding RNAs ... A-to-I candidates from RNA-Seq experiments as well as guidelines to improve the RNA editing detection in non-coding RNAs, with ... A-to-I candidates from RNA-Seq experiments as well as guidelines to improve the RNA editing detection in non-coding RNAs, with ...
RNA editing blood biomarkers for predicting mood alterations in HCV patients | SpringerLink
In total, NGS sequencing identified up to 27 adenosines which were identified to be actively edited by A-to-I RNA editing above ... A-I RNA editing activity on the phosphodiesterase 8A (PDE8A) gene, a previously identified RNA editing hotspot in the context ... As observed for the RNA editing level on the B site of the PDE8A intron 9, the RNA editing activity response to IFN-α was ... Interestingly, IFN-α induces gene expression of the RNA editing enzyme ADAR1-1 (ADAR1a-p150) and alters overall RNA editing ...
Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells
This RNA editing is induced by cellular crowding and mitochondrial respiratory inhibition to promote adaptation to hypoxic ... APOBEC3G is an endogenous RNA editing enzyme in primary natural killer cells and lymphoma cell lines. ... However, de novo induction of RNA editing in response to environmental factors is an uncommon phenomenon. While APOBEC3A edits ... APOBEC3G is an endogenous RNA editing enzyme in primary natural killer cells and lymphoma cell lines. This RNA editing is ...
Genes | Free Full-Text | Functions of the RNA Editing Enzyme ADAR1 and Their Relevance to Human Diseases
Novel identifications of long noncoding RNA and retrotransposons as editing targets further expand the effects of A-to-I ... Besides editing, ADAR1 also interacts with other dsRNA-binding proteins in editing-independent manners. Elucidating the disease ... Furthermore, editing of noncoding sequences, like microRNAs, can regulate protein expression, while editing of Alu sequences ... Editing in both coding and noncoding sequences results in diseases ranging from cancers to neurological abnormalities. ...
Accurate identification of human Alu and non-Alu RNA editing sites
As compared with previous methods, our approach identified a large number of Alu and non-Alu RNA editing sites with high ... We developed a computational framework to robustly identify RNA editing sites using transcriptome and genome deep-sequencing ... We also found that editing of non-Alu sites appears to be dependent on nearby edited Alu sites, possibly through the locally ... Accurate identification of human Alu and non-Alu RNA editing sites Nat Methods. 2012 Jun;9(6):579-81. doi: 10.1038/nmeth.1982. ...
RNA Editing Repairs Rett Syndrome Mutation in Mouse Model
Building on early success in the lab dish, the team wanted to find out whether it was possible to edit the MECP2 RNA in nerve ... Using a mouse model of Rett, the researchers used RNA editing to correct a mutation in MeCP2 by rewriting the RNA to code for a ... "The study is the first example of RNA editing in a mouse model of a neurological disease, and therefore a considerable step ... "It is encouraging that this RNA editing approach seems to be efficacious in different types of neurons in the brain," said Gail ...
Rice MPR25 encodes a pentatricopeptide repeat protein and is essential for RNA editing of nad5 transcripts in mitochondria<...
Direct sequencing revealed that the mpr25 mutant fails to edit a C-U RNA editing site at nucleotide 1580 of nad5, which encodes ... Direct sequencing revealed that the mpr25 mutant fails to edit a C-U RNA editing site at nucleotide 1580 of nad5, which encodes ... Direct sequencing revealed that the mpr25 mutant fails to edit a C-U RNA editing site at nucleotide 1580 of nad5, which encodes ... Direct sequencing revealed that the mpr25 mutant fails to edit a C-U RNA editing site at nucleotide 1580 of nad5, which encodes ...
Cas9-guide RNA ribonucleoprotein-induced genome editing in the industrial green alga Coccomyxa sp. strain KJ | Biotechnology...
For introduction of Cas9-guide RNA ribonucleoprotein into strain KJ cells, we used an electroporator with a short (2.5 ms) ... editing of strain KJ by intracellular delivery of a ribonucleoprotein complex comprising recombinant Cas9 protein and guide RNA ... Consequently, the development of new genetic tools including genome editing that are applicable to this strain is highly ... Our study shows applicability of DNA-free genome editing in Coccomyxa, which may be applicable in other Trebouxiophyceae ...
Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola. | Appl Environ...
There was no overlap between differentially expressed and differentially edited genes, suggesting that these may provide F. ... We examined both gene expression (transcription levels) and RNA editing (posttranscriptional modification of RNA, which can ... We analyzed the gene expression levels and RNA editing profiles of F. pinicola from submerged cultures with ground wood powder ... In contrast, the suites of genes subject to RNA editing were much less affected by culture conditions. These findings highlight ...
Cas9 nuclease expression reagents
... is complexed with two RNAs called the CRISPR RNA (crRNA) and the trans-activating crRNA (tracrRNA), it forms an endonuclease ... is based on the Type II CRISPR-Cas9 system from the bacteria Streptococcus pyogenes which can be engineered and adapted to edit ... Edit-R synthetic guide RNA. An illustration of the Edit-R CRISPR-Cas9 components required for gene editing:plasmid expressing ... The level of editing was calculated using densitometry (% editing). An increase in % gene editing is observed in the sorted ...
New CRISPR genome editing system offers a wide range of versatility in human cells | Broad Institute
The pegRNA also contains additional RNA nucleotides encoding the new edited sequence. To transfer this information, the reverse ... Prime editing differs from previous genome-editing systems in that it uses RNA to direct the insertion of new DNA sequences in ... Edits made to order. In the Nature paper, the team demonstrated prime editings ability to precisely correct gene variants that ... "Prime editing" combines two key proteins and a new RNA to make targeted insertions, deletions, and all possible single-letter ...
Octopus Cold Adaptation Surprises Scientists | The Institute for Creation Research
But with RNA editing, the octopuses can rapidly diversify and fill watery environments of various temperatures. University of ... And the specific edits change just those points along the protein that affect speed, thereby adjusting the speed of the whole ... RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses. Science. 335 (6070): 848-851. ... Thus, in these [protein] channels greater species diversity is generated by RNA editing than by gene mutations, according to ...
New genetic editing powers discovered in squid
This is the first time that edits to genetic information have been observed outside of the nucleus of an animal cell. ... scientists have discovered that squid massively edit their own genetic instructions not only within the nucleus of their ... "But we thought all the RNA editing happened in in the nucleus, and then the modified messenger RNAs are exported out to the ... through prolific RNA editing More information: Isabel C Vallecillo-Viejo et al, Spatially regulated editing of genetic ...
Q&A: Why geneticists say it's wrong to edit the DNA of embryos to protect them against HIV - Los Angeles Times
An embryo receives a small dose of gene-editing proteins and RNA in a sperm injection microscope in a Shenzhen laboratory. ... Q&A: Why geneticists say its wrong to edit the DNA of embryos to protect them against HIV ... But the gene-editing work thats generally underway in labs is not being done on embryos, as was reportedly done here. Its ... I do think there will be a time when this kind of gene-editing technique is used. But theres definitely an ethical issue with ...
Cas9 nuclease protein NLS
Edit-R synthetic guide RNA. Gene editing with Cas9 Nuclease protein NLS and guide RNA is performed by co-transfecting all ... Synthetic guide RNAs and Cas9 nuclease protein electroporated as RNP. Guide RNAs and Cas9 protein were combined to form an RNP ... DharmaFECT transfection reagents are highly recommended for use with Edit-R™ gene editing reagents and should be purchased ... Edit-R Cas9 nuclease protein and synthetic guide RNA transfection - Quick Protocol ...
Expanding the CRISPR - Trinity News
By targeting RNA, C2c2 wont make permanent edits to the genome. This allows it to make temporary, adjustable changes to a gene ... Editing of these "germ-line" cells can produce permanent genetic changes which are then inherited by future generations. These ... CRISPR edited cells prevent cancer from hijacking PD-1. A similar trial has been approved in the United States and is due to ... It could be just the beginning, the first of many gene editing tools to be plucked from the microbial dark matter. CRISPR-Cas9 ...
Researchers Use CRISPR-Carrying Nanoparticles To Edit Genomes
MIT develops nanoparticles to deliver the CRISPR genome-editing system and specifically modify genes, eliminating the need to ... "Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing," Nature Biotechnology, ... Using this approach, in which the guide RNA was still delivered by a virus, the researchers were able to edit the target gene ... To deliver the guide RNAs, they first had to chemically modify the RNA to protect it from enzymes in the body that would ...
CRISPR algorithm predicts how well gene editing will work - Scope
Researchers at Stanford have created an algorithm that predicts how likely CRISPR gene editing will yield off-target mutations. ... During a CRISPR-based edit, a strand of molecules called a guide RNA leads the DNA-slicing protein Cas9 to the section of DNA ... Its more like editing a word document with your eyes closed. You know what you want to edit and where you want to edit, but ... The same is true for gene editing using CRISPR. Cutting DNA or inserting new genetic material can trigger new unintended edits ...
RNA Control and Regulation
RNA Modifications; Nuclear Localization of RNA; Quality Control & Editing; RNA & Gene Regulation; Cotranscriptional Splicing; ... Edited by Terri Grodzicker, Cold Spring Harbor Laboratory; David Stewart, Cold Spring Harbor Laboratory; Bruce Stillman, Cold ... Long Noncoding RNAs; RNA & Development; Membrane-Less Organelles; Phase Separation; RNA-Based Diseases; and Novel RNA Functions ... Chromatin and RNA. Small RNA Function in Plants: From Chromatin to the Next Generation. Jean-Sébastian Parent, Filipe Borges, ...
Loyola University Chicago Archives - Innovation Toronto
For First Time, Scientists Use CRISPR-Cas9 to Target RNA in Live Cells
San Diego School of Medicine have now achieved this by applying the popular DNA-editing technique CRISPR-Cas9 to RNA. ... Scientists have long sought an efficient method for targeting RNA- intermediary genetic material that carries the genetic code ... Efforts to edit and measure DNA - as a means to alter protein production, study the underlying biology and correct defects to ... San Diego School of Medicine have now achieved this by applying the popular DNA-editing technique CRISPR-Cas9 to RNA. ...
360°-view technology key to Volvo Cars' goal of no fatal accidents by 2020 - Innovation Toronto
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How CRISPR works-Cas enzymes, guide RNAs, and RNPs | IDT
CRISPR technology for genome editing. Information about design, delivery, knockouts and homology-directed repair (HDR) ... and genome editing takes place inside cells. For a quantitative assessment, DNA from edited cells can be sequenced by next ... This editing technology relies on Cas enzymes and guide RNAs (gRNAs) that are part of the bacterial immune systems found in ... Cas9 guide RNA design tool. Select from our predesigned gRNAs targeting human, mouse, rat, zebrafish, or nematode genes. For ...
Introduction to CRISPR screening | IDT
A high degree of similarity in CRISPR-Cas9 editing efficiency is found between 2-part guide RNAs and single guide RNAs » ... Furthermore, most of the CRISPR-edited cells will also be killed, because most genes in the genome are not drug-sensitivity ... but this is not CRISPR guide RNA. This is viral RNA, which is much too long for a Cas enzyme to use in genome editing. When ... Complete reagent set for successful genome editing; modified RNAs and RNP delivery give higher on-target potency. ...
Publications | Max Planck Institute
... such as Xist and Air are discussed in light of recent research of mechanisms regulating chromatin marking and RNA editing. The ... In Kids Cut & Break, all 34 clips are edited into a single file, which plays the clips successively with 5 seconds of black ... Some RNA networks may trace back to an early stage when there was just RNA and proteins, the RNP‑world; before DNA. ... Daly, T., Chen, X. S., & Penny, D. (2011). How old are RNA networks? In L. J. Collins (. Ed.. ), RNA infrastructure and ...
Search | Page 10 | The Embryo Project Encyclopedia
Church and his team used RNA-guided Cas 9 technology to edit the genetic information in human cells. ... CRISPR /Cas9-mediated Gene Editing in Human Tripronuclear Zygotes (2015), by Junjiu Huang et al.. In 2015, Junjiu Huang and ... in which they detailed their use of RNA-guided Cas 9 to genetically modify genes in human cells. Researchers use RNA-guided Cas ... RNA-Guided Human Genome Engineering via Cas 9 (2013), by Prashant Mali, Luhan Yang, Kevin M. Esvelt, John Aach, Marc Guell, ...
Search | Page 10 | The Embryo Project Encyclopedia
Church and his team used RNA-guided Cas 9 technology to edit the genetic information in human cells. ... CRISPR /Cas9-mediated Gene Editing in Human Tripronuclear Zygotes (2015), by Junjiu Huang et al.. In 2015, Junjiu Huang and ... in which they detailed their use of RNA-guided Cas 9 to genetically modify genes in human cells. Researchers use RNA-guided Cas ... RNA-Guided Human Genome Engineering via Cas 9 (2013), by Prashant Mali, Luhan Yang, Kevin M. Esvelt, John Aach, Marc Guell, ...
Is gene editing kooky futurist crap, or too expensive for mass distribution? | The Straight Dope | Savannah News, Events,...
The CRISPR-Cas9 editing process still looks like the revolutionary development its been touted as over the last four years, ... in which the guide RNA gets confused by multiple similar DNA strings and the wrong gene gets edited; even when the enzyme finds ... So in CRISPR-Cas9 editing, researchers create guide RNA sequences that match parts of whatever gene they want to alter and use ... I keep hearing about the bright future of gene editing, involving something called CRISPR. Ive seen claims it could cure ...
molecular biology | Lunatic Laboratories
Squid prolifically edit RNA to enrich their DNA. DNA, its what makes us, well us! Not that long ago, before we sequenced human ... RNA, rna editing, science, squid , Leave a comment ... Now, a new study suggests that bacteriophages made of RNA - a ... Want to make a virus? Its easy: combine one molecule of genomic nucleic acid, either DNA or RNA, and a handful of proteins, ... preventing rotation of the RNA polymerase along the DNA helix (orange arrow). Image credit goes to: Nadezhda S. Gerasimova et ...
Non-canonical translation in RNA viruses | Microbiology Society
In addition, RNA viruses have very compact genomes and are under intense selective pressure to optimize usage of the available ... However, many RNA virus transcripts have marked structural differences from cellular mRNAs that preclude canonical translation ... Together, these features have driven the evolution of a plethora of non-canonical translational mechanisms in RNA viruses that ... Here, we review the mechanisms utilized by RNA viruses of eukaryotes, focusing on internal ribosome entry, leaky scanning, non- ...
EnzymeCRISPREnzymesGRNATranscriptDeaminasesMicroRNAsDouble-stranded RNA-specific adenosineMiRNAsSubstratesPolymeraseTRNAsTranscriptome-wideMutationsMammalianChloroplastsADAR-mediated RNAChloroplastCas9-guide RNAPathwaysPost-transcriptional2017DiversityMolecularMetazoanTargetsMechanistically diverse typesPrecursorStructuresCodonsLigaseSerotonin 2c receptorAdenosinesCleavageDiversificationAZIN1 RNAOccurRegulationRegulateInduceZhangGeneticSitesOccursFunctionalMammalsDsRNAPlastidMechanismPathogenesis
- A team led by Jennifer Doudna, biochemist and leading authority on the CRISPR/Cas9 complex, showed how the Cas9 enzyme can work with short DNA sequences known as "PAM," for protospacer adjacent motif, to identify and bind with specific site of single-stranded RNA (ssRNA). (eurekalert.org)
- Cas9 - Cas stands for CRISPR-assisted - is an RNA-guided enzyme that handles the sniping of DNA strands at the specified sequence site. (eurekalert.org)
- The two two dark humps in the top row (representing fly RNA) are missing in flies that lack the enzyme to edit RNA (middle row) and missing in the DNA. (eurekalert.org)
- The "master list" totals 3,581 sites in which the enzyme ADAR might swap an "A" nucleotide for a "G" in an RNA molecule. (eurekalert.org)
- They compared the sequenced RNA of a population of fruit flies to their sequenced DNA and to the RNA of another population of flies engineered to lack the ADAR editing enzyme. (eurekalert.org)
- The REPAIR system is based on Cas13, an enzyme that does the same, but for RNA. (fiercebiotech.com)
- The scientists created a deactivated version of the Cas13 enzyme, PspCas13b, which binds precisely to a stretch of RNA, but does not cut it. (fiercebiotech.com)
- They combined the enzyme with the protein ADAR2, which switches A to I in RNA transcripts, and then improved the tool to cut down on off-target effects. (fiercebiotech.com)
- The most widely used cytosine base editors (CBEs) induce deamination of DNA cytosines using the rat APOBEC1 enzyme, which is targeted by a linked Cas protein-guide RNA complex 3,4 . (massgeneral.org)
- CRISPR technology comprises a growing family of tools that can manipulate genes and their expression, including by targeting DNA with the enzymes Cas9 and Cas12 and targeting RNA with the enzyme Cas13. (sciencecodex.com)
- Zhang and his team, including first co-authors Omar Abudayyeh and Jonathan Gootenberg(both now McGovern fellows), made use of a deactivated Cas13 to guide RESCUE to targeted cytosine bases on RNA transcripts, and used a novel, evolved, programmable enzyme to convert unwanted cytosine into uridine -- thereby directing a change in the RNA instructions. (sciencecodex.com)
- A study in Nature Communications finds that an enzyme that edits RNA may loosen the genome's control over invasive snippets of DNA that affect how genes are expressed. (healthcanal.com)
- In the new paper, scientists show that an enzyme called ADAR, which edits RNA in humans, flies, and many other creatures, edits double-stranded RNAs. (healthcanal.com)
- Interestingly, IFN-α induces gene expression of the RNA editing enzyme ADAR1-1 (ADAR1a-p150) and alters overall RNA editing activity. (springer.com)
- APOBEC3G is an endogenous RNA editing enzyme in primary natural killer cells and lymphoma cell lines. (nih.gov)
- found that the RNA-editing enzyme ADAR supports the activity of FAK. (sciencemag.org)
- We found that CREB regulates ADAR1, an enzyme involved in RNA editing," said Bar-Eli, whose study findings appear in this month's issue of Nature Cell Biology . (healthcanal.com)
- RNA editing by adenosine deamination is catalyzed by members of an enzyme family known as a denosine d e a minases that act on R NA (ADARs) ( 6 ). (pubmedcentralcanada.ca)
- Additionally, the expression of RNA editing enzyme (ADAR1) was also upregulated in cancerous tissues compared to normal mucosa, and positively correlated with AZIN1 editing levels. (aacrjournals.org)
- Herein we show that the adenosine-toinosine editing enzyme ADAR1 undergoes gene amplification in non-small cancer cell lines and primary tumors in association with higher levels of the corresponding mRNA and protein. (csic.es)
- RNA editing in Trypanosoma brucei mitochondria produces mature mRNAs by a series of enzyme-catalyzed reactions that specifically insert or delete uridylates in association with a macromolecular complex. (asm.org)
- To address these questions, the researchers packaged a mouse Mecp2 RNA guide and human editing enzyme (the "editase") in a viral vector and introduced it directly into the hippocampus, a well-studied brain structure associated with learning and memory. (technologynetworks.com)
- We will do this by analyzing altered RNA processing in mouse brain deficient for the editing enzyme. (neurodegenerationresearch.eu)
- 2004) Liver disintegration in the mouse embryo caused by deficiency in the RNA-editing enzyme ADAR1. (oalib.com)
- A second discovery, published in Science, uses a new CRISPR enzyme to edit not only DNA but also RNA, the chemical messenger that living things use to turn DNA code into the proteins that are the building blocks of living bodies. (forbes.com)
- Challenges to practical use in the clinic or in agriculture include delivery (the editing enzyme is very large) and precision, since edits occur at sites neighboring the desired position. (forbes.com)
- A team of researchers with Berkeley Lab and the University of California (UC) Berkeley has demonstrated a means by which the CRISPR/Cas9 protein complex can be programmed to recognize and cleave RNA at sequence-specific target sites. (eurekalert.org)
- They are designating this RNA-targeting CRISPR/Cas9 complex as RCas9. (eurekalert.org)
- Just as Cas9 can be used to cut or bind DNA in a sequence-specific manner, RCas9 can cut or bind RNA in a sequence-specific manner," says Mitchell O'Connell, a member of Doudna's research group and the lead author of a paper in Nature that describes this research titled "Programmable RNA recognition and cleavage by CRISPR/Cas9. (eurekalert.org)
- NEW YORK (GenomeWeb) - A team of researchers from Massachusetts General Hospital led by Keith Joung has reported in a new study that CRISPR-Cas base editing technology can induce transcriptome-wide off-target RNA editing in human cells, along with off-target DNA edits. (genomeweb.com)
- A team from the Broad Institute has devised a CRISPR-based system that targets RNA in a way that makes reversible changes to DNA possible. (fiercebiotech.com)
- A Massachusetts General Hospital (MGH) research team reports that several of the recently developed CRISPR base editors, which create targeted changes in a single DNA base, can induce widespread off-target effects in RNA, extending beyond the targeted DNA. (massgeneral.org)
- In contrast to CRISPR-Cas gene-editing nucleases, which induce targeted double-strand DNA breaks in order to make genetic changes, CRISPR base editors are able to change a single nucleotide in a DNA strand without inducing such breaks. (massgeneral.org)
- Joung notes that investigating any potential impact of these RNA effects on experimental and clinical applications of CRISPR base editing is an important next step his team is taking. (massgeneral.org)
- In addition, some cell types, such as neurons, are difficult to edit using CRISPR/Cas9-mediated editing, and new strategies are needed to treat devastating diseases that affect the brain. (sciencecodex.com)
- Genome editing using standard tools (ZFN, TALEN, and CRISPR/Cas9) rely on double strand breaks to edit the genome. (g3journal.org)
- The clustered regularly interspaced short palindromic repeat (CRISPR) system has been widely used for site-specific genome editing in various organisms and cell lines ( Sander and Joung 2014 ). (g3journal.org)
- clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing has still not been developed and may be a technique that is more effective than other genome editing techniques. (biomedcentral.com)
- Effective CRISPR guide RNAs guaranteed to edit the gene of interest. (horizondiscovery.com)
- A newly discovered form of Crispr may eventually be used to modify human RNA. (nytimes.com)
- The groundbreaking thing about this work is that it now opens up the RNA world to Crispr," said Oliver Rackham, a synthetic biologist at the University of Western Australia who was not involved in the study. (nytimes.com)
- Once they discovered some candidates, they joined forces with Feng Zhang of M.I.T., who published one of the first studies on using Crispr to edit human DNA. (nytimes.com)
- 2016. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. (nap.edu)
- The techniques both build on the discovery of CRISPR, a bacterial immune system that biologists have hacked into a gene-editing tool. (forbes.com)
- Researchers working in the lab of Feng Zhang were looking for a way to use CRISPR in cells in the brain, which don't divide and therefore can't be edited just by making cuts and waiting for the cell to fix the damage during replication. (forbes.com)
- The paper shows that editing of the RNA with CRISPR is possible. (forbes.com)
- The DNA editing paper is indeed interesting because it expands the kinds of targeted changes that can be made in DNA without introducing breaks,' said Jennifer Doudna, a UC Berkeley professor who is widely credited with co-discovering CRISPR. (forbes.com)
- They used Cas9 enzymes from the bacterium Streptococcus pyogenes to perform a variety of in vitro cleavage experiments using a panel of RNA and DNA targets. (eurekalert.org)
- The most common type of RNA editing is A-to-I editing by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. (nature.com)
- Fig. 1: A-to-I RNA editing is catalysed by ADAR enzymes and is the most common type of RNA editing in Metazoa. (nature.com)
- To investigate the possibility of reducing or eliminating unwanted RNA edits, the MGH team screened 16 editors with engineered versions of the deaminase enzymes, identifying two that were as efficient as the original version in inducing on-target DNA effects while inducing markedly fewer RNA edits. (massgeneral.org)
- These results have implications for the use of base editors in both research and clinical settings, illustrate the feasibility of engineering improved variants with reduced RNA editing activities, and suggest the need to more fully define and characterize the RNA off-target effects of deaminase enzymes in base editor platforms. (massgeneral.org)
- Deamination is brought about by the action of specific editing enzymes, termed ADAR (adenosine deaminase acting on RNA). (springer.com)
- Expression levels of editing enzymes and their isoforms can explain some, but not all of this variation. (biomedcentral.com)
- Compositions and methods for expanding CD34+ cells, performing research related to cancer stem cells, RNA-editing enzymes and for monitoring, diagnosing and treating, ameliorating and preventing diseases such as cancers or inflammatory diseases. (patents.com)
- 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)
- 2003) Dynamic association of RNA-editing enzymes with the nucleolus. (oalib.com)
- It is catalyzed by the family of adenosine deaminases acting on RNA (ADAR) enzymes [ 3 ] and is considered to be more active in the brain [ 4 ]. (biomedcentral.com)
- Virtually all editing activity is located in non-coding repetitive elements, which readily pair with inverted copies of the same repeat to form double-stranded RNA (dsRNA) substrates that are the preferred targets of the editing enzymes [ 28 ]. (biomedcentral.com)
- like protein enzymes , RNA enzymes ( ribozymes ) can catalyze (start or accelerate) chemical reactions that are critical for life . (wikipedia.org)
- Protein enzymes may have come to replace RNA-based ribozymes as biocatalysts because their greater abundance and diversity of monomers makes them more versatile. (wikipedia.org)
- Using a mitochondrial fraction enriched for in vitro RNA editing activity, we produced several monoclonal antibodies that are specific for a 21-kDa guide RNA (gRNA) binding protein initially identified by UV cross-linking. (asm.org)
- The antibodies cause a supershift of previously identified gRNA-specific ribonucleoprotein complexes and immunoprecipitate in vitro RNA editing activities that insert and delete uridylates. (asm.org)
- RNA editing produces mature mRNAs in the mitochondria of trypanosomatids by guide RNA (gRNA)-directed posttranscriptional insertion and deletion of uridylates (U's) ( 2 ). (asm.org)
- The editing window of BE3 reached up to 13 bases (from C1 to C13 in the range of gRNA) in B. mori . (g3journal.org)
- Under the direction of a guide RNA (gRNA), the Cas9 nuclease binds to an opened DNA strand that pairs with the gRNA and induces a double-strand break (DSB). (g3journal.org)
- Every editing site was determined by guide RNA (gRNA) which located in the same RNA. (nii.ac.jp)
- The mechanism of the editosome involves an endonucleolytic cut at the mismatch point between the guide RNA and the unedited transcript. (wikipedia.org)
- As a consequence, the editosome can edit only in a 3' to 5' direction along the primary RNA transcript. (wikipedia.org)
- Therefore, a RNA transcript requiring extensive editing will need more than one guide RNA and editosome complex. (wikipedia.org)
- This finding has the potential to transform the study of RNA function by paving the way for direct RNA transcript detection, analysis and manipulation. (eurekalert.org)
- Our results reveal a fundamental connection between PAM binding and substrate selection by RCas9, and highlight the utility of RCas9 for programmable RNA transcript recognition without the need for genetically introduced tags. (eurekalert.org)
- Together, these data suggest a complex regulation of the RNA-editing process beyond transcript expression levels. (biomedcentral.com)
- Indeed, it has recently been shown that the pri-miRNA transcript of human miRNA miR-22 is subject to A-to-I RNA editing in a number of human and mouse tissues [ 31 ]. (biomedcentral.com)
- In the mitochondria of A. formosae, 30 editing sites were observed in 420 bases region of cox1 transcript. (nii.ac.jp)
- No RNA editing was found in the mitochondrial cox1 transcript from 4 kinds of liverworts. (nii.ac.jp)
- Editing in the coding region of a transcript can lead to an amino acid substitution (recoding), resulting in a novel protein isoform and, possibly, an altered protein function. (biomedcentral.com)
- Additionally, editing in the non-coding region of a transcript can affect splicing, microRNA targeting, RNA degradation, translation, and other important cellular processes [ 2 ]. (biomedcentral.com)
- Bass, B. L. RNA editing by adenosine deaminases that act on RNA. (nature.com)
- Nishikura, K. Functions and regulation of RNA editing by ADAR deaminases. (nature.com)
- Adenosine deamination by adenosine deaminases that act on RNA (ADAR) seemingly only affects metazoan nuclear encoded RNAs. (frontiersin.org)
- Collectively, our data show for the first time that RNA-guided cytidine deaminases are capable of programmable single and multiplex base editing in an invertebrate model. (g3journal.org)
Double-stranded RNA-specific adenosine1
- Manipulation of the miRNAs by silencing the naturally occurring or wild-type version of a miRNA and overexpressing an "edited" miRNA confirmed the significance of RNA editing in tumor growth and metastasis. (healthcanal.com)
- We have conducted a survey of RNA editing of miRNAs from ten human tissues by sequence comparison of PCR products derived from matched genomic DNA and total cDNA from the same individual. (biomedcentral.com)
- Our results indicate that RNA editing increases the diversity of miRNAs and their targets, and hence may modulate miRNA function. (biomedcentral.com)
- Pri-miRNAs contain a short double-stranded RNA (dsRNA) stem-loop formed between the miRNA sequence and its adjacent complementary sequence. (biomedcentral.com)
- Therefore, the double-stranded precursors of miRNAs may be substrates for A-to-I editing. (biomedcentral.com)
- In this study we have systematically investigated the presence of RNA editing in miRNAs. (biomedcentral.com)
- To search for RNA-editing sites in human miRNAs, PCR product sequencing was performed from matched total cDNA and genomic DNA isolated from adult human brain, heart, liver, lung, ovary, placenta, skeletal muscle, small intestine, spleen and testis. (biomedcentral.com)
- Given these many mechanisms for regulating editing levels, generally or for specific substrates, there are many ways to generate a diverse editing landscape. (biomedcentral.com)
- Table S1 [see Additional file 1 ] summarizes the recoding of ADAR substrates by RNA editing, the amino acid position, and the physiological changes in channel properties and expression. (biomedcentral.com)
- Meanwhile, this strategy can be used to precisely mimic human pathologies by efficiently inducing nonsense or missense mutations as well as RNA mis-splicing in rabbit. (nature.com)
- In this study, we have discovered an unexpected role for GUN1 in plastid RNA editing, as gun1 mutations affect RNA-editing efficiency at multiple sites in plastids during retrograde signaling. (pnas.org)
- The team tested their tool against RNA mutations that cause Fanconi anemia and X-linked nephrogenic diabetes insipidus, finding that the system repaired the mutations. (fiercebiotech.com)
- We engineered two CBE variants bearing mutations in rat APOBEC1 that substantially decreased the number of RNA edits (by more than 390-fold and more than 3,800-fold) in human cells. (massgeneral.org)
- The team took the new platform into human cells, showing that they could target natural RNAs in the cell, as well as 24 clinically relevant mutations in synthetic RNAs. (sciencecodex.com)
- ABEs convert one DNA base pair into another, allowing for the repair of mutations in some cell types without generating undesired editing effects. (phys.org)
- Overall, we report a list of A-to-I editing events that recently originated through G-to-A mutations in primates, representing a valuable resource to investigate the features and evolutionary significance of A-to-I editing events at the population and species levels. (springer.com)
- As a strategy to restore the normal function of MECP2 , the single-base RNA editing approach of swapping out A and G could address about 40% of all known mutations that cause Rett Syndrome, Sinnamon says. (technologynetworks.com)
- Previous studies of the specificity of CBEs have identified off-target DNA edits in mammalian cells 5,6 . (massgeneral.org)
- Currently, most of the identified targets of A-to-I RNA editing are found in the mammalian nervous system, such as the ion channels and neurotransmitter receptors that play crucial roles in electrical excitability and signal transduction. (biomedcentral.com)
- 4 ) make a strong case that RNA editing in chloroplasts contributes to a type of chloroplast-to-nucleus signaling defined by the genomes uncoupled ( gun ) mutants in Arabidopsis . (pnas.org)
- Our study uncovers a role for GUN1 in the regulation of RNA-editing efficiency in damaged chloroplasts and suggests that MORF2 is involved in retrograde signaling. (pnas.org)
- Retrograde signaling and posttranscriptional RNA editing are important regulatory processes for chloroplast development and function in flowering plants. (pnas.org)
- Finally, we observe that chloroplast RNA editing appears to be completely absent in horsetails (Equisetales), the sister clade of all other monilophytes. (biomedcentral.com)
- MODOMICS: a database of RNA modification pathways. (nature.com)
- There is a need to discover new potential actionable genetic lesions, to which end, non-conventional cancer pathways, such as RNA editing, are worth exploring. (csic.es)
- RNA editing is essential for the normal development of plant and is involved in a wide variety of biological pathways. (biomedcentral.com)
- RNA editing is an important co/post-transcriptional molecular process able to modify RNAs by nucleotide insertions/deletions or substitutions. (frontiersin.org)
- RNA editing is a site specific, post transcriptional modification of RNA. (frontiersin.org)
- In human cancers, aberrant post-transcriptional modifications, such as alternative splicing and RNA editing, may lead to tumour specific transcriptome diversity. (bmj.com)
- F11R is subjected to RNA editing, a post-transcriptional modification which affects RNA structure, stability, localization, translation and splicing. (oalib.com)
- RNA-editing processes show great molecular diversity, and some appear to be evolutionarily recent acquisitions that arose independently. (wikipedia.org)
- Fig. 5: RNA editing generates transcriptomic diversity. (nature.com)
- Numerous examples of RNAs known to be edited are provided throughout the volume, but most importantly, the book highlights the amazing mechanistic diversity found among the various types of RNA editing. (oup.com)
- help to dispel any remaining ignorance for students and researchers who are interested in RNA processing and mechanisms for increasing genetic diversity alike. (oup.com)
- However, the transcribed messenger RNAs are extensively edited, creating functional diversity. (mysciencework.com)
- We were quite surprised at the number - tens of thousands - of RNA edits and the frequency of these alterations that we observed with the two classes of base editors," says lead author Julian Grünewald, MD, MGH Molecular Pathology and Harvard Medical School. (massgeneral.org)
- ADAR in humans functions the same way it does in flies, and double-stranded RNAs are made in humans the same way," said Reenan, professor of biology in the Department of Molecular Biology, Cell Biology and Biochemistry. (healthcanal.com)
- The Frontiers in Molecular Biology series has provided a tight little volume, RNA Editing , which provides one-stop-shopping for some of the most current data available on this fascinating subject. (oup.com)
- Chapters guide readers through state- of-the art methodologies to investigate RNA editing through wet and dry approaches.Written in the highly successful Methods in Molecular Biology 扎朶佌肰抑泰幱台series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. (war-films.com)
Mechanistically diverse types2
- We show, through reporter RNA constructs, that RNA splice sites suppress editing of precursor RNAs when placed proximal or distal to the editing site. (biochemj.org)
- Processed RNAs were edited more efficiently than precursor RNAs. (biochemj.org)
- The HIV-1 Rev-Rev response element ('RRE') interaction was utilized to uncouple the commitment of precursor RNAs to the spliceosome assembly pathway and associated nuclear-export pathway. (biochemj.org)
- Compared to sites of mild editing, ultra-editing occurs primarily in Alu-rich regions, where potential base pairing with neighboring, inverted Alus creates particularly long double-stranded RNA structures. (nih.gov)
- Aside from the propensity of RNA substrate to form hairpin structures, little is known about other mechanisms regulating this more selective form of editing. (biomedcentral.com)
- Clusters of editing sites are abundant in repetitive genomic regions that putatively form double-stranded RNA (dsRNA) structures and are rarely seen in coding regions. (biomedcentral.com)
- Inosines are interpreted as guanosines and hence, this type of editing can change codons, alter splice patterns, or influence the fate of an RNA. (frontiersin.org)
- This process can be so extensive that most of the coding sequence, as well as the initiation and termination codons, results from RNA editing ( 1 , 11 , 27 , 28 , 30 ). (asm.org)
- Thus band IV ligase is needed to seal RNAs in U‐deletion. (embopress.org)
- U‐insertion does not appear to require band IV, so it might use the other ligase of the editing complex. (embopress.org)
- Furthermore, band IV ligase was also found to serve an RNA repair function, both in vitro and in vivo . (embopress.org)
Serotonin 2c receptor1
- A-to-I editing can be specific (a single adenosine is edited within the stretch of dsRNA) or promiscuous (up to 50% of the adenosines are edited). (wikipedia.org)
- Four out of seven edited adenosines were in the mature miRNA and were predicted to change the target sites in 3' untranslated regions. (biomedcentral.com)
- Although the extent of A-to-I editing was low (less than 5% across all adenosines analyzed), targeted adenosines were at positions predicted to influence the biogenesis and function of miR-22. (biomedcentral.com)
- In addition, we performed a series of functional assays to elucidate the functional role of AZIN1 RNA editing in CRC pathogenesis. (aacrjournals.org)
- Results: Using RESSqPCR, AZIN1 RNA editing levels were analyzed in two CRC cohorts. (aacrjournals.org)
- Taken together, these results highlight the oncogenic role of AZIN1 RNA editing in CRC. (aacrjournals.org)
- Conclusion: Our systematic and comprehensive study, which is first of its kind, reveals that AZIN1 RNA editing is novel epigenetic alteration that promotes an oncogenic behavior in colorectal cancer. (aacrjournals.org)
- In addition to increasing our knowledge of the regulation of plant organellar RNA editing under stress conditions, this research uncovers a possible link between retrograde signaling and plastid RNA editing. (pnas.org)
- However, at present, very little is known about the regulation of editing across tissues, and individuals. (biomedcentral.com)
- Importantly, comprehensive characterization of this subset of RNA editome, if exists, could advance the evolutionary and functional interrogation of primate RNA editing regulation in the following regards. (springer.com)
- Finally, we want to continue our analysis on the role of RNA editing in the regulation of the GABA-A receptor during brain development. (neurodegenerationresearch.eu)
- Most investigation of off-target base editing has focused on DNA, but we have found that this technology can induce large numbers of RNA alterations as well," says J. Keith Joung, MD, PhD , of the MGH Department of Pathology and senior author of the Nature report. (massgeneral.org)
- This led the MGH team to investigate whether it might induce off-target RNA effects. (massgeneral.org)
- Using RNA-Seq we will investigate if A-to-I editing can induce alternative splicing and polyadenylation, an event that previously has been ignored. (neurodegenerationresearch.eu)
- This new ability to edit RNA opens up more potential opportunities to recover that function and treat many diseases, in almost any kind of cell," said Feng Zhang, core institute member at the Broad Institute, in a press release. (fiercebiotech.com)
- McGovern Institute Investigator and Broad Institute of MIT and Harvard core member Feng Zhang and his team have now developed one such strategy, called RESCUE (RNA Editing for Specific C to U Exchange), described in the journal Science . (sciencecodex.com)
- Zhang and colleagues introduced the risk-associated APOE4 RNA into cells and showed that RESCUE can convert its signature Cs to an APOE2 sequence, essentially converting a risk to a non-risk variant. (sciencecodex.com)
- Zhang Z, Carmichael GG (2001) The fate of dsRNA in the nucleus: a p54(nrb)-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs. (oalib.com)
- To exploit the vast potential of microbes, scientists must be able to precisely edit their genetic information. (eurekalert.org)
- A genomic error that causes Rett Syndrome, a serious lifelong neurological disorder, can be corrected in the brains of mice by rewriting the genetic instructions carried by the RNA. (technologynetworks.com)
- Researchers have invented two new techniques that expand the ability of human beings to edit the genetic code of living things, potentially paving the way for new medical and agricultural applications. (forbes.com)
- She says the new technique could be very useful in making genetic edits without causing re-arrangements of the DNA, a problem with current techniques. (forbes.com)
- The second technique makes it possible to edit a whole other species of genetic chemical: RNA. (forbes.com)
- It's possible that life started as RNA, and some viruses, like HIV, use the chemical as their genetic material. (forbes.com)
- Target base editing (red arrows), target sequence (black), PAM region (green), target sites (red), mutant amino acid (underlined) and amino acid mutation type are indicated. (nature.com)
- PROVIDENCE, R.I. [Brown University] -- A research team centered at Brown University has compiled the largest and most stringently validated list of RNA editing sites in the fruit fly Drosophila melanogaster , a stalwart of biological research. (eurekalert.org)
- In fact, Reenan was co-author of a paper in Science 10 years ago that made a splash with only 56 new editing sites which at the time, more than doubled the number of known sites in the entire field. (eurekalert.org)
- Several more recent attempts to catalog RNA editing sites have yielded larger catalogs, but those contained many errors (the paper provides a comparison between the new list and previous efforts such as ModENCODE). (eurekalert.org)
- Kleinberger, Y. & Eisenberg, E. Large-scale analysis of structural, sequence and thermodynamic characteristics of A-to-I RNA editing sites in human Alu repeats. (nature.com)
- We detected 760 ESTs containing 15,646 editing sites (more than 20 sites per EST, on average), of which 13,668 are novel. (nih.gov)
- Ultra-editing sites are underrepresented in old Alu subfamilies, tend to be non-conserved, and avoid exons, suggesting that ultra-editing is usually deleterious. (nih.gov)
- They identified specific editing sites and signs of editing on the double stranded RNA. (healthcanal.com)
- Some editing sites, such as adenosine (A)-to-U editing loci, were found to be surrounded by peculiar elements. (biomedcentral.com)
- Both concluded that the majority of these sites were false positives (If these authors are wondering why they're not cited in our comment, it's because Science didn't let me add the citations during the editing process, sorry! (genomesunzipped.org)
- The C nucleotide being edited at the three sites is underlined. (plantphysiol.org)
- Population genetics analyses of the focal editing sites further reveal that a portion of these young editing events are evolutionarily significant, indicating general functional relevance for at least a fraction of these sites. (springer.com)
- Number of editing sites were 20 to 4 per 1000 bases, and no silent editing was observed. (nii.ac.jp)
- 2004) Systematic identification of abundant A-to-I editing sites in the human transcriptome. (oalib.com)
- Technical requirements have limited systematic mapping of editing sites to a small number of organisms. (biomedcentral.com)
- Here, we apply a computational procedure to search for RNA-sequencing reads containing clusters of editing sites in 21 diverse organisms. (biomedcentral.com)
- The number of editing sites varies considerably across species. (biomedcentral.com)
- All of the editing sites were C-to-U conversions, which mainly occurred in the second codon position, biased towards to the U_A context, and caused an increase in hydrophobic amino acids. (biomedcentral.com)
- Our single-cell in situ sequencing method has proved useful to study the complex landscape of RNA editing and our results indicate that this complexity arises due to distinct mechanisms of regulating individual RNA editing sites, acting both regionally and in specific cell types. (biomedcentral.com)
- unligated RNAs cleaved at U‐deletion sites accumulated. (embopress.org)
- Currently, a total of 4 editing sites that result in amino acid changes have been identified, namely glutamate to arginine (Q/R), arginine to glycine (R/G), isoleucine to valine (I/V), and tyrosine to cysteine (Y/C). (biomedcentral.com)
- In addition to its functional role, AZIN1 editing levels may be one of the important facilitators of adenoma-carcinoma sequence in CRC and serve as an important clinical biomarker in this disease. (aacrjournals.org)
- However, the functional consequences of many of these RNA editing events are still unknown. (neurodegenerationresearch.eu)