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 22.214.171.124.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 126.96.36.199.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 188.8.131.52.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 184.108.40.206.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 220.127.116.11.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 18.104.22.168.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.
Lim, K; Furuta, Y; Kobayashi, I (October 2012). "Large variations in bacterial ribosomal RNA genes". Molecular Biology and ... The ribosomes in chloroplasts are similar to bacterial ribosomes. Because so many chloroplast genes have been moved to the ... Genes from a chloroplast and nuclear genes indicating the presence of a chloroplast have been found in Helicosporidium even if ... From genomes that probably originally contained over 3000 genes only about 130 genes remain in the chloroplasts of contemporary ...
Human gene is no longer transcribed into RNA. Alasdair J Edgar (2005) Mice have a transcribed L-threonine aldolase/GLY1 gene, ... but the human GLY1 gene is a non-processed pseudogene. BMC Genomics March 2005, 6:32. pdf Bell SC; Turner JM (1973). "Bacterial ... Human gene contains two single nucleotide deletions causing frameshifts and premature stop codons. Also, the encoded protein ... Humans also have the remnants of the gene, coding this enzyme (GLY1), however it is damaged by past mutations and inactive. ...
Operon vic is an operon made of five genes, located on the bacterial chromosome. The only known gene is vicA, the fourth gene ... The hyp codifies for an RNA-helicase; mutants for this gene are hypervirulent. Also, hyp is involved in post transcriptional ... The fas is an operon made of six genes (orf 1-6) and a regulatory gene, fasR. Because deletions of some fas genes give a non- ... The att is an operon composed of nine genes: attR, a transcriptional regulator, attX, a gene including domains for ...
Narberhaus F (2010). "Translational control of bacterial heat shock and virulence genes by temperature-sensing mRNAs". RNA ... Some bacterial heat shock proteins are upregulated via a mechanism involving RNA thermometers such as the FourU thermometer, ... Gata4 is an essential gene responsible for cardiac morphogenesis. It also regulates the gene expression of hspb7 and hspb12. ... Expression of the hspb4 gene, which codes for alpha crystallin, increases considerably in the lens in response to heat shock. ...
"Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ". Proceedings of the National Academy of Sciences ... Bacterial small RNAs have been identified as components of many regulatory networks. Twenty sRNAs were experimentally ... When genes of unknown function on CII are disrupted, many types of auxotrophy result, emphasizing that the CII is not merely a ... Many genes are duplicated between the two chromosomes but appear to be differentially regulated. Moreover, many of the open ...
The rpoB gene encodes the β subunit of bacterial RNA polymerase. It codes for 1342 amino acids, making it the second-largest ... "Structural mechanism for rifampicin inhibition of bacterial RNA polymerase". Cell. 104 (6): 901-12. doi:10.1016/S0092-8674(01) ... Case RJ, Boucher Y, Dahllöf I, Holmström C, Doolittle WF, Kjelleberg S (2007). "Use of 16S rRNA and rpoB genes as molecular ... Some bacteria contain multiple copies of the 16S rRNA gene, which is commonly used as the molecular marker to study phylogeny. ...
Plasmids of bacteria are a transferable genetic element through bacterial conjugation. This is a mechanism of horizontal gene ... An RNA transcript of MGEs is copied by reverse transcriptase. Then, the DNA sequence can be inserted back to a random location ... Gene duplication events can also happen through the mechanism of MGEs. MGEs can also cause mutations in protein coding regions ... Newly acquired genes though this mechanism can increase fitness by gaining new or additional functions. On the other hand, MGEs ...
The tuberactinomycins target bacterial ribosomes, binding RNA and disrupting bacterial protein biosynthesis. It is produced by ... that binds to RNA and inhibits prokaryotic protein synthesis and certain forms of RNA splicing. The gene cluster for viomycin ... In addition to these ORFs, the structure contains the resistance gene vph. The following is a summary of the ORFs and their ... It is proposed that the viomycin gene cluster includes 36.3 kb of contiguous DNA that encodes 20 open reading frames (ORFs) ...
Retrotransposons are transposons that first transcribe the moving gene sequence into RNA. This RNA then gets retro transcribed ... Here she discovered that mu transposons behave similarly to transposons and retrotransposons involved with bacterial resistance ... The ability of these genes to move around is extremely important in DNA's flexibility and ensuring that there are different ... DNA transposons are also known jumping genes because they move around the chromosome and can insert themselves into different ...
The small RNAs may regulate bacterial and host genes. Highly conserved intragenic region sRNA called ncrwmel02 was also ... "The Bacterial Symbiont Wolbachia Induces Resistance to RNA Viral Infections in Drosophila melanogaster". PLOS Biology. 6 (12): ... It is the first bacteriophage implicated in frequent lateral transfer between the genomes of bacterial endosymbionts. Gene ... Genome Discovered Inside Another's-Bacterial to Animal Gene Transfers Now Shown to be Widespread, with Implications for ...
RNA polymerase is then used to generate long double stranded RNA that is homologous to the target-gene cDNA. This RNA is ... RNA interference rescue by bacterial artificial chromosome transgenesis in mammalian tissue culture cells. Proc Natl Acad Sci U ... Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells ... Efficient RNA interference in zebrafish embryos using synthesized with SP6 RNA polymerase. Dev Growth Differ. 47(5), 323-31 ( ...
Woo, P.C.; Lau,Chan,Fung,Tang,Yuen (2005). "Clostridium bacteramia characterized by 16S ribosomal RNA gene sequencing". Journal ... Antibiotic treatment can also alter the balance of microbiota causing pathogenic bacterial growth. In humans, one of the first ... cadaveris is via molecular techniques utilizing ribosomal RNA gene sequencing. Infections due to C. cadaveris are rare and ... Translocation and proliferation of gut flora such as C. cadaveris allow for these organisms to serve as bacterial indicators ...
The E. faecalis genome consists of 3.22 million base pairs with 3,113 protein-coding genes. Bacterial small RNAs play important ... Anti-Q RNA Ryan KJ, Ray CG, eds. (2004). Sherris Medical Microbiology (4th ed.). McGraw Hill. pp. 294--5. ISBN 0-8385-8529-9. ... 11 small RNAs have been experimentally characterised in E. faecalis V583 and detected in various growth phases. Five of them ... Type strain of Enterococcus faecalis at BacDive - the Bacterial Diversity Metadatabase. ...
"Large variations in bacterial ribosomal RNA genes". Molecular Biology and Evolution. 29 (10): 2937-48. doi:10.1093/molbev/ ... Gene content and protein synthesis. The chloroplast genome most commonly includes around 100 genes that code for a ... 4.4 Gene content and protein synthesis *4.4.1 Chloroplast genome reduction and gene transfer ... Chloroplasts may contain 60-100 genes whereas cyanobacteria often have more than 1500 genes in their genome. Recently, a ...
"Detecting protein-DNA interactions in vivo: distribution of RNA polymerase on specific bacterial genes". Proc Natl Acad Sci U S ... Following lysis of cross-linked cells and immunoprecipitation of bacterial RNA polymerase, DNA associated with enriched RNA ... A year later they used the same methodology to study distribution of eukaryotic RNA polymerase II on fruit fly heat shock genes ... Gilmour DS, Lis JT (August 1985). "In vivo interactions of RNA polymerase II with genes of Drosophila melanogaster". Mol. Cell ...
"A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes". Trends Genet. 15 (11): ... The FMN riboswitch (also known as RFN element) is a highly conserved RNA element that is found frequently in the 5'- ... Winkler, WC; Cohen-Chalamish S; Breaker RR (2002). "An mRNA structure that controls gene expression by binding FMN". Proc Natl ... Serganov A, Huang L, Patel DJ (2009). "Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch". Nature ...
Distribution of RNA polymerase on specific bacterial genes". Proceedings of the National Academy of Sciences. 81: 4275-4279. ... Ribosomal protein genes bound by this protein had a tendency to use a particular motif with a stronger consensus sequence. ... Other genes often used clusters of weaker consensus motifs, possibly to achieve a similar occupancy. Binding motifs of CTCF ... in high definition Resolving transcription factor binding High-resolution chromatin immunoprecipitation Important Gene- ...
The Histidine operon leader is an RNA element found in the bacterial histidine operon. At least 6 amino acid operons are known ... In each a leader sequence of 150-200 bp is found upstream of the first gene in the operon. This leader sequence can assume two ... This allows RNA polymerase to transcribe the operon. Kolter R, Yanofsky C (1982). "Attenuation in amino acid biosynthetic ... The terminator structure is recognised as a termination signal for RNA polymerase and the operon is not transcribed. This ...
Winkler W, Nahvi A, Breaker RR (2002). "Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression ... manA RNA motif, pfl RNA motif, ydaO/yuaA leader, yjdF RNA motif, ykkC-yxkD leader (and related ykkC-III RNA motif) and the yybP ... "Metabolite-binding RNA domains are present in the genes of eukaryotes". RNA. 9 (6): 644-7. doi:10.1261/rna.5090103. PMC 1370431 ... "A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes". Trends Genet. 15 (11): ...
Winkler, W; Nahvi A; Breaker RR (2002). "Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene ... "Metabolite-binding RNA domains are present in the genes of eukaryotes". RNA. 9 (6): 644-647. doi:10.1261/rna.5090103. PMC ... New genes and regulatory mechanisms". J Biol Chem. 277 (50): 48949-48959. doi:10.1074/jbc.M208965200. PMID 12376536. Miranda- ... The TPP riboswitch, also known as the THI element and Thi-box riboswitch, is a highly conserved RNA secondary structure. It ...
Giangrossi, M. (2010). "A novel antisense RNA regulates at transcriptional level the virulence gene icsA of Shigella flexneri ... The activity of the incA protein is crucial for spreading of the bacterial pathogen in the host cells. ... It is a first regulatory RNA characterised in S. flexneri. The RNA is 450 nucleotides long (which makes it one of the largest ... RnaG is a small regulatory non-coding RNA encoded by the virulence plasmid of Shigella flexneri, a Gram-negative pathogenic ...
The ribosomal RNA and transfer RNA genes belong to the class of middle repetitive DNA. Inverted repeat Ussery, David W.; ... Wassenaar, Trudy; Borini, Stefano (2008-12-22). "Word Frequencies, Repeats, and Repeat-related Structures in Bacterial Genomes ...
Bacillus cibi strain AIMST Ngme2 16S ribosomal RNA gene, partial sequence. NCBI. Bacillus cibi strain AIMST Nmae9 16S ribosomal ... Identification of bacterial endophytes isolated from eight Nepenthes species and their screening for cytokinin-like compounds. ... RNA gene, partial sequence. NCBI. Bacillus flexus strain AIMST Nae10 16S ribosomal RNA gene, partial sequence. NCBI. Bacillus ... Bacillus cereus strain AIMST Nalbe1 16S ribosomal RNA gene, partial sequence. NCBI. Bacillus cereus strain AIMST Nalbe7 16S ...
The bacterial glycine riboswitch is an RNA element that can bind the amino acid glycine. Glycine riboswitches usually consist ... It is thought that when glycine is in excess it will bind to both aptamers to activate these genes and facilitate glycine ... Kwon, M; Strobel SA (2008). "Chemical basis of glycine riboswitch cooperativity". RNA. 14 (1): 25-34. doi:10.1261/rna.771608. ... RNA. 18 (3): 496-507. doi:10.1261/rna.031286.111. PMC 3285937 . PMID 22279151. Butler, EB; Xiong Y; Wang J; Strobel SA (2011 ...
The toxic effects of the protein are neutralised by the RNA gene. One example is the ToxIN system from the bacterial plant ... Gene regulation - some toxins act as a means of general repression of gene expression while others are more specific. Growth ... February 2011). "A processed noncoding RNA regulates an altruistic bacterial antiviral system". Nat. Struct. Mol. Biol. 18 (2 ... Toxin-antitoxin genes are often transferred through horizontal gene transfer and are associated with pathogenic bacteria, ...
The viral RNA polymerase, encoded by the L gene, partially uncoats the nucleocapsid and transcribes the genes into positive- ... balance as well as treating any bacterial infections that may develop. Dialysis may be needed for kidney failure, and ... Ebolaviruses contain single-stranded, non-infectious RNA genomes. Ebolavirus genomes contain seven genes including 3'-UTR- ... Finding the virus, viral RNA, or antibodies in blood. Differential diagnosis. Malaria, cholera, typhoid fever, meningitis, ...
Bacterial control of host gene expression through RNA polymerase II. Nataliya Lutay,1 Ines Ambite,1 Jenny Grönberg Hernandez,1 ... Effects on RNA Pol II-dependent transcription. RNA Pol II controls eukaryotic gene expression through mRNA precursors, most ... Such bacterial modulation of host gene expression may be essential to sustain asymptomatic bacterial carriage by ensuring that ... MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 2004;23(20):4051-4060.. View this article via: PubMed CrossRef ...
RNA can also serve in these capacities. For example, RNA has sufficient structural plasticity to form ribozyme1,2 and receptor3 ... It has also been proposed7,8,9,10,11,12 that certain messenger RNAs might use allosteric mechanisms to mediate regulatory ... mRNA-effector complex adopts a distinct structure that sequesters the ribosome-binding site and leads to a reduction in gene ... Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. *Wade Winkler1. , ...
Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction ... Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction ... Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction ... Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction ...
DNA-dependent RNA polymerase subunits of Group I, which incl … ... subunits of bacterial DNA-dependent RNA polymerases (DdRp), ... Evolution of Bacterial RNA Polymerase: Implications for Large-Scale Bacterial Phylogeny, Domain Accretion, and Horizontal Gene ... Comparative analysis of the domain architectures of the beta, beta, and sigma(70) subunits of bacterial DNA-dependent RNA ... horizontal transfer of complete genes for all or some of the subunits, resulting in displacement of the ancestral genes, might ...
Construction and recovery of viable retroviral genomes carrying a bacterial suppressor transfer RNA gene ... Construction and recovery of viable retroviral genomes carrying a bacterial suppressor transfer RNA gene ... Construction and recovery of viable retroviral genomes carrying a bacterial suppressor transfer RNA gene ... Construction and recovery of viable retroviral genomes carrying a bacterial suppressor transfer RNA gene ...
There is thus the need for computational methods to design optimal bacterial 16S primers able to take into account the ... We also experimentally validated three of the primer pairs identified by our method on multiple bacterial species, belonging to ... Results confirm the predicted efficiency and the ability to maximize the number of different bacterial 16S sequences matched by ... minimizes the differences in the number of primers matching each bacterial 16S sequence. Our algorithm can be applied to any ...
Bacterial Strains.. An isogenic set of strains carrying wild-type or mutant alleles of fur [fur∷kan, obtained from G. Storz (19 ... there is a complete correlation between sRNAs that act by means of RNA-RNA pairing and Hfq use, consistent with RNA-RNA pairing ... A small RNA, RyhB, was found as part of a genomewide search for novel small RNAs in Escherichia coli. The RyhB 90-nt RNA down- ... Similarly, the bfr gene is the second gene in an operon; we have not thus far examined the synthesis of the upstream gene (bfd ...
PR-1, BGL2, and PR-5 gene-specific probes were used for RNA gel blot analysis of the indicated plants, with the UBQ5 gene- ... PR-1 and PDF1.2 gene-specific probes were used for RNA gel blot analysis, and the 18S ribosomal subunit gene-specific probe was ... Uncoupling PR Gene Expression from NPR1 and Bacterial Resistance: Characterization of the Dominant Arabidopsis cpr6-1 Mutant. ... The table below each RNA gel blot describes the fold induction of gene expression for each sample relative to that of the wild ...
The gene in this thermophile was systematically replaced with a diverse array of heterologous genes, resulting in the discovery ... However, a growing number of reports suggest the occurrence of horizontal gene transfer, raising genealogical questions. Here ... Remarkably, cold-adapted mutants were obtained carrying chimeric or full-length heterologous genes, indicating that horizontal ... of various genes that supported growth, some of which were from different phyla. Moreover, numerous functional chimeras were ...
Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation ... RNA-DIRECTED RNA POLYMERASE. A, B, C. 665. Pseudomonas phage phi6. Mutation(s): 0 Gene Names: P2. EC: 22.214.171.124. ... Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation ... Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation ...
RNA / chemistry * RNA, Bacterial / chemistry * RNA, Ribosomal, 16S / chemistry * RNA, Ribosomal, 16S / genetics* ... Classification and identification of propionibacteria based on ribosomal RNA genes and PCR Syst Appl Microbiol. 1998 Jun;21(2): ...
SC contributed to the experiment set-up and was responsible for bacterial cultures and RNA extractions; she participated in ... Similarly, the class Ib ribonucleotide reductase (RNR)-encoding genes (nrdHIEF) are probably important for bacterial life in ... This allows bacterial pathogens to (i) adapt their gene transcription profiles in response to environmental cues sensed during ... an approach for discovering bacterial genes involved in septicaemic plague. Microbiology. 2007;153:3112-3124. doi: 10.1099/mic. ...
... the bacterial communities associated with threes type of samples was investigated using 16S rRNA gene and environmental shotgun ... a phenomenon which previous studies have indicated is caused by a temperature induced bacterial disease. In order to better ... algal metabolites which are antagonists of bacterial quorum sensing. This study reveals the complex shift in the community ... Ribosomal RNA Is the Subject Area "Ribosomal RNA" applicable to this article? Yes. No. ...
... putative defense and fiber biosynthesis-related genes that are highly expressed in... ... Amplified RNA. BAC. Bacterial artificial chromosome. CaMV35S. Cauliflower mosaic virus 35S promoter ... Promoters (Pro) of these genes were isolated and fused to the β-glucuronidase (GUS) reporter gene. Transient and stable ... a rice anther-specific gene is required for male fertility and its promoter sequence directs tissue-specific gene expression in ...
Purchase RNA Polymerase and Associated Factors, Part C, Volume 370 - 1st Edition. Print Book & E-Book. ISBN 9780121822736, ... Construction and purification of RNA polymerases. *DNA microarrays and bacterial gene expression ... RNA polymerase is molecule important to gene transcription. Along with associated factors, RNA polymerase is part of the ... RNA Polymerase and Associated Factors, Part C, Volume 370 1st Edition. Write a review ...
Ermolenko, D. N., & Makhatadze, G. I. (2002). Bacterial cold-shock proteins. Cellular and Molecular Life Sciences, 59, 1902- ... Derry, J. M., Kerns, J. A., & Francke, U. (1995). RBM3, a novel human gene in Xp11.23 with a putative RNA-binding domain. Human ... Alternative Promoters Regulate Cold Inducible RNA-Binding (CIRP) Gene Expression and Enhance Transgene Expression in Mammalian ... Cold-shock Cold-inducible RNA-binding protein Promoters Transgene expression Gene expression ...
... using the clone library method with a 16S ribosomal RNA (rRNA) gene analysis in 42 patients from a pneumonia registry who had ... We evaluated the bacterial microbiota in bronchoalveolar lavage fluid (BALF) ... patients among the detected bacterial phylotypes, but a minor population (the percentage of clones ≤ 10 %) in 19 (67.9 %) of 28 ... cultivation and 16S ribosomal RNA gene analysis of bronchoalveolar lavage fluid Back to article ...
Previous message: Need Input on Northern With Bacterial RNA *Next message: Killer gene ... Need Input on Northern With Bacterial RNA. Shahram Mori smori at nmsu.edu Mon Mar 13 02:39:14 EST 1995 * ... RNA. : Does anyone know of any compounds I could add to my growing culture : to slow the RNA turnover rate without killing my ... Northerns on bacterial RNA. I have been using the Chomczynski (sp?) : and Sacchi procedure (AGPC procedure, Analytical Biochem ...
Archaebacterial RNA polymerase subunit D (gene rpoD).. Helmann JD, Chamberlin MJ. Structure and function of bacterial sigma ... In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA ... Schizosaccharomyces pombe rpb3 subunit from RNA polymerase II.. *Mammalian RPB3 (or RPB33) (gene POLR2C) from RNA polymerase II ... Short name: DNA-dir_RNA_pol_30-40kDasu_CS Description. DNA-directed RNA polymerases EC:126.96.36.199 (also known as DNA-dependent RNA ...
Expression of a bacterial gene in mammalian cells. Science 209: 1422-1427.. *CrossRef, ... Factors governing the expression of a bacterial gene in mammalian cells. Mol Cell Biol 1: 449-459.. *PubMed, ... mRNA-based gene transfer as a tool for gene and cell therapy. Curr Opin Mol Ther 9: 423-431.. *PubMed, ... Math1: an essential gene for the generation of inner ear hair cells. Science 284: 1837-1841.. *CrossRef, ...
"Large variations in bacterial ribosomal RNA genes". Molecular Biology and Evolution. 29 (10): 2937-48. doi:10.1093/molbev/ ... Gene content and protein synthesis. The chloroplast genome most commonly includes around 100 genes that code for a ... 4.4 Gene content and protein synthesis *4.4.1 Chloroplast genome reduction and gene transfer ... Chloroplasts may contain 60-100 genes whereas cyanobacteria often have more than 1500 genes in their genome. Recently, a ...
... and initiation of transcription of heat shock genes, including numerous global transcriptional regulators and genes involved in ... This sigma factor is involved in regulation of expression of heat shock genes. Intracellular concentration of free RpoH protein ... Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then ... increases in response to heat shock, which causes association with RNA polymerase (RNAP) ...
Detection of bacterial 16S rRNA genes levels above the qPCR detection level occurred only on PND6 and only for some of the ... We hypothesized that the nature of bacterial colonization affects mucus gene regulation in early life. We thus analyzed the ... Quantification of 16S rRNA genes was performed to obtain a measure for amounts of colonized bacteria. We found a microbiota- ... In summary, our data show that development of the expression of genes encoding secreted (Muc2/Tff3) and membrane-bound (Muc1/ ...
RNA Gene), , including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene ... Summaries for PIR34956 Gene GeneCards Summary for PIR34956 Gene PIR34956 is an RNA Gene, and is affiliated with the piRNA class ... Publications for PIR34956 Gene * A germline-specific class of small RNAs binds mammalian Piwi proteins. (PMID: 16751776) Girard ... The GeneCards human gene database index: 2 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z ...
RNA Gene), Uncharacterized LOC105372202, including: function, proteins, disorders, pathways, orthologs, and expression. ... Summaries for LOC105372202 Gene GeneCards Summary for LOC105372202 Gene LOC105372202 (Uncharacterized LOC105372202) is an RNA ... The GeneCards human gene database index: 2 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z ... No data available for DME Specific Peptides for LOC105372202 Gene Domains & Families for LOC105372202 Gene Graphical View of ...
Ribosomal RNA geneProteinGenomeDegradationEnzymesGeneticsSequencesSubunitRegulatoryCRISPRRibosomeBindsPromotersMoleculeInitiationMammalian cellsMoleculesSRNAsMolecularCatalyticAnalysesRibosomesIsolationAbundanceStabilityEnzyme2018VirulenceFluorescenceDownstreamEndogenousFunctionalHost gene expressionReplicationTranscriptomeRegulate the expressionOrganismRRNA genesBiogenesisCharacterizeColi
- Targeted amplicon sequencing of the 16S ribosomal RNA gene is one of the key tools for studying microbial diversity. (biomedcentral.com)
- A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. (nih.gov)
- 16S ribosomal RNA gene sequence and phylogeny of toxic Microcystis sp. (semanticscholar.org)
- The researchers focused on a ribosomal RNA gene called SSU rRNA, which can reliably identify bacterial species. (heraldnet.com)
- RyhB requires the RNA-binding protein, Hfq, for activity. (pnas.org)
- Along with associated factors, RNA polymerase is part of the process in which RNA is transcribed to produce a protein. (elsevier.com)
- Conjugation stage-specific protein cnjC from Tetrahymena thermophila, which may be a stage-specific RNA polymerase subunit. (ebi.ac.uk)
- Intracellular concentration of free RpoH protein increases in response to heat shock, which causes association with RNA polymerase (RNAP) and initiation of transcription of heat shock genes, including numerous global transcriptional regulators and genes involved in maintaining membrane functionality and homeostasis. (uniprot.org)
- 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)
- One of the challenges in studying abiogenesis is that the system of reproduction and metabolism utilized by all extant life involves three distinct types of interdependent macromolecules ( DNA , RNA , and protein ). (wikipedia.org)
- The transcription factors regulatory factor X (RFX), cAMP response element binding protein (CREB), and nuclear factor-Y (NF-Y) bind to proximal promoter conserved upstream sequences (termed X1, X2, and Y boxes, respectively) of all MHC-II genes (for review see references 3 - 5 ), and are required and constitutively expressed, but are not sufficient, to initiate transcription of MHC-II. (rupress.org)
- It is becoming increasingly evident that longer forms of non-protein-coding RNAs (ncRNAs) are involved directly in regulating gene expression and epigenetic states. (keystonesymposia.org)
- We analyzed cDNA libraries from developing endosperm of the B73 maize inbred line to evaluate the expression of storage protein genes. (plantcell.org)
- Knowledge of expressed storage protein genes allowed the development of DNA and antibody probes that distinguish between closely related gene family members. (plantcell.org)
- A sandwich-like dual-fluorescence reporter was further constructed by fusing the Bc3-5 RNA gene between the two fluorescence protein genes amcyan and turborfp. (nih.gov)
- Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase: BIOCHEMICAL AND STRUCTURAL STUDIES. (nih.gov)
- Members of the Swi2/Snf2 (switch/sucrose non-fermentable) family depend on their ATPase activity to mobilize nucleic acid-protein complexes for gene expression. (nih.gov)
- The RNA polymerase (RNAP) binding protein A (RbpA) contributes to the formation of stable RNAP-promoter open complexes (RP o ) and is essential for viability in mycobacteria. (asm.org)
- We demonstrated that decreases in protein overproduction levels are not due to significant plasmid loss nor to mutations arising on the plasmid, but instead largely are attributable to chromosomal mutations that diminish the level of functional T7 RNA polymerase, resulting in decreased expression from the plasmid. (biomedcentral.com)
- Isolation of plasmid DNA from non-expressing strains and reintroduction of the plasmid into a T7 RNA polymerase-producing strain such as BL21(λDE3) reproducibly restored high level protein production. (biomedcentral.com)
- In the most desirable situation, expression of the cloned gene will consume the majority of the cellular resources, such that at the time of harvest the target protein makes up the bulk of the cell content. (biomedcentral.com)
- The target protein is encoded on a plasmid in which the gene has been cloned so that transcription will be driven by the T7 RNA polymerase. (biomedcentral.com)
- We initially examined the conditions required for optimal target protein production from pET plasmids because we observed inconsistent results upon induction of plasmid-borne genes. (biomedcentral.com)
- The YPS3 gene of Histoplasma capsulatum encodes a protein that is both surface localized in the cell wall of H. capsulatum and released into the culture medium. (asm.org)
- We isolated the causal gene, which encodes a protein homologous to DNA-dependent RNA polymerase (RNAP) III subunit C4 (RPC4). (g3journal.org)
- A Rho factor will bind to the RNA in a region, called the transcription terminator pause site-- this is rich in guanine and cytosine and is after the part of the gene that codes for protein. (wikibooks.org)
- There is now a synthesized bacterial protein and ribosomal subunits that can help in further translations. (wikibooks.org)
- By studying a bacterial ortholog of one such protein, the ring-shaped Ro60 autoantigen, they discovered that this protein is tethered by noncoding "Y RNA" to a ring-shaped nuclease, forming a double-ringed ribonucleoprotein machine specialized for structured RNA degradation. (cancer.gov)
- For example, UV irradiation causes RNA-protein crosslinks and increases transcription of retrotransposons and satellite RNAs. (cancer.gov)
- We analyze hundreds of bacterial genomes and find that the coding sequences of highly expressed genes systematically contain fewer SD sequences than expected, yielding a robust correlation between the normalized occurrence of SD sites and protein abundances across a range of bacterial taxa. (g3journal.org)
- RNAIII from S. epidermidis , S. warneri , or S. simulans , when introduced into an RNAIII-deficient mutant of S. aureus (WA400), completely repressed transcription of protein A but stimulated transcription of alpha-hemolysin ( hla ) and serine protease ( sasp ) genes less efficiently. (asm.org)
- Intact protein can be recovered from RNA later solution-stabilized samples for use in downstream applications such as western blotting or 2D gel analysis. (thermofisher.com)
- Joung and Sander, 2013 ), are based on protein-DNA interactions, whereas a third technology, clustered regularly interspaced short palindromic repeats ( CRISPR )/CRISPR-associated9 (Cas9) endonuclease ( Liu and Fan, 2014 ), is an RNA-guided DNA endonuclease system. (plantphysiol.org)
- This is an adeno-associated virus containing the DNA coding for the RNA guide, the Cas9 protein derived from Campylobacter jejuni and the fluorescent reporter protein (GFP). (eurekalert.org)
- Cas9 is the "gene scissors" protein: It creates cuts on the target gene in precise locations indicated by the guide RNA. (eurekalert.org)
- It has 984 aminoacids and it can be packed in AAV together with more than one guide RNAs as well as with a fluorescent reporter protein. (eurekalert.org)
- In order to use a bacterial protein for gene editing, scientists had to optimize some aspects of the technique. (eurekalert.org)
- Afterwards, IBS scientists packaged the new CRISPR-Cas9 complex into AAV, together with two guide RNAs and a fluorescent reporter protein, to mutate genes in mice's muscles and eyes. (eurekalert.org)
- The construction of a retrovirus that stably carries a suppressor transfer RNA gene from Escherichia coli has allowed facile recovery of the viral genome in vectors marked with amber mutations. (sciencemag.org)
- This has been particularly true for long noncoding RNAs and is even more the case for molecules transcribed from "parasitic" retrotransposons-repetitive DNA sequences inserted throughout the genome. (phys.org)
- RNA-sequencing, or RNA-seq, is used to analyze expression levels of all transcripts in a genome, including sRNAs. (wikipedia.org)
- Noise is hence a genome-wide phenomenon that arises from the stochastic nature of the biochemical reactions that take place during gene expression and the relatively low abundance of the molecules involved. (biochemsoctrans.org)
- Altogether, Golic+ realizes high-efficiency ends-out gene targeting in ovarian cystoblasts, which can be readily scaled up to achieve high-throughput genome editing. (genetics.org)
- Ambion now introduces a new technology, MICROB Enrich , that enables whole genome microarray expression analyses of bacterial RNA after host-bacterial interactions. (bio-medicine.org)
- A shotgun microarray study which analyzed approximately one-third of the genes in the Histoplasma genome found nearly 500 genes that are differentially expressed in the mold and yeast phases ( 11 ). (asm.org)
- Phylogenetic analysis demonstrated that gene duplication of RPC4 at DGS1 and DGS2 was a recent event that occurred after divergence of the ancestral population of Oryza from other Poaceae or during diversification of AA-genome species. (g3journal.org)
- Now, professor Emmanuelle Charpentiers work group has scoured the genome of several hundred bacterial species in the search of CRISPR-Cas genes and has made several discoveries. (infectioncontroltoday.com)
- Horizontal gene transfer and genome evolution in Methanosarcina, BMC Evolutionary Biology, 15(1):102,2015. (iitp.ru)
- Bacterial genome plasticity is mandatory to adapt and respond to environmental threats, including antibiotic stress. (asm.org)
- During the past 12 years, there has been rapid development of genome-editing strategies that make it possible to directly target regions of genes in a DNA sequence-specific manner. (plantphysiol.org)
- These genes are additional to existing core genome copper resistance mechanisms, and are not found in typical S. aureus lineages, but are increasingly identified in emerging pathogenic isolates. (findaphd.com)
- Scientists at the Center for Genome Engineering, within the Institute for Basic Science (IBS), in collaboration with KIM Eunji (ToolGen Inc.) and KIM Jeong Hun (Seoul National University) have engineered the smallest CRISPR-Cas9 to date, delivered it to the muscle cells and in the eyes of mice via adeno-associated viruses (AAV) and used it to modify a gene causing blindness. (eurekalert.org)
- AAV is an efficient and safe vector to express a gene of interest in vivo and has been used widely in gene therapy," explains KIM Jin-Soo, director of the IBS Center for Genome Engineering and corresponding author of the study. (eurekalert.org)
- By paving the way to the application of CjCas9 against 'undruggable' genes or non-coding sequences, this technology can broaden the range of therapeutic targets, making the entire human genome potentially druggable. (eurekalert.org)
- These small RNAs form ribonucleoprotein complexes with Hfq and RNase E. The regulatory outcomes of the RNase E/Hfq/small RNA-containing ribonucleoprotein complex (sRNP) are rapid degradation of target mRNAs and translational inhibition. (pnas.org)
- Previously, we found that the truncated RNase E lacking the C-terminal scaffold region no longer supports the rapid degradation of target mRNAs mediated by SgrS or RyhB RNA ( 9 , 12 ). (pnas.org)
- These small RNAs are then incorporated into AGO-containing RNA-induced silencing complexes (RISCs) to serve as the sequence specificity in RNA degradation, translational inhibition, or heterochromatin formation ( Bologna and Voinnet, 2014 ). (frontiersin.org)
- We discovered that retroviruses package these RNAs from a previously unknown pathway in which newly made RNAs are exported to the cytoplasm for degradation. (cancer.gov)
- The tissues thaw without risk of RNA degradation. (thermofisher.com)
- How this results in depression of gene expression was shown recently by Winkler and colleagues to be due to RNase J1-mediated degradation of the downstream cleavage product ( Fig. 1A ) [ 7 ]. (pubmedcentralcanada.ca)
- Thus, glmS gene expression is regulated by a combination of metabolite-mediated ribozyme cleavage and exonucleolytic degradation. (pubmedcentralcanada.ca)
- Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli. (weizmann.ac.il)
- We study small-RNA downregulation to elucidate its effects on noise in the iron homeostasis network of Escherichia coli In this network, the small-RNA RyhB undergoes stoichiometric degradation with the transcripts of target genes in response to iron stress. (weizmann.ac.il)
- These include two other genes encoding enzymes in the tricarboxylic acid cycle, acnA and fumA , two ferritin genes, ftnA and bfr , and a gene for superoxide dismutase, sodB . (pnas.org)
- Type VI CRISPR systems, including the enzymes Cas13a/C2c2 and Cas13b, target RNA rather than DNA. (addgene.org)
- Type VI enzymes that function in mammalian cells can be used to attentuate RNA levels. (addgene.org)
- Like all ancient biomolecules, ribosomes are RNA enzymes. (scienceblogs.com)
- Thirteen of these genes provide instructions for making enzymes involved in oxidative phosphorylation. (medlineplus.gov)
- Two for the Price of One: RNA Modification Enzymes as Chaperones. (cancer.gov)
- The accuracy of this approach strongly depends on the choice of primer pairs and, in particular, on the balance between efficiency, specificity and sensitivity in the amplification of the different bacterial 16S sequences contained in a sample. (biomedcentral.com)
- Results confirm the predicted efficiency and the ability to maximize the number of different bacterial 16S sequences matched by primers. (biomedcentral.com)
- However, our knowledge over unculturable bacterial sequences is rapidly growing thanks to Next-Generation Sequencing (NGS), a technology that is continuously evolving and improving [ 3 ]. (biomedcentral.com)
- Fur is a repressor that binds to specific DNA sequences called Fur boxes, usually located in the promoter region of a target gene. (pnas.org)
- The classes of RNA molecules encoded by DNA sequences previously considered non functional may play a vital role in cell stress responses, and could one day lead to cancer treatments. (phys.org)
- After validation of RNA quality, the RNA is subjected to cDNA synthesis via primers that specifically match adapter sequences, or through random priming. (biomedcentral.com)
- 10 yr ago in which upstream sequences of the Eα gene were deleted displayed aberrant MHC-II expression patterns, suggesting that the deleted elements may serve a role in tissue-specific expression ( 9 , 10 ). (rupress.org)
- The 16S rRNA sequences revealed a different bacterial community compared with 16S rRNA gene-based results across all samples, and this difference depended on the sampling device. (cdc.gov)
- In addition, a number of bacterial taxa exhibited higher abundance in the 16S rRNA gene sequences than in 16S rRNA sequences, which suggests the potential activities of certain microbes in airborne phase. (cdc.gov)
- In 1992, Margaret Kidwell, an evolutionary geneticist, and José Ribeiro, a vector biologist, proposed using transposable elements , mobile sequences of DNA, as a mechanism to drive an engineered gene into a mosquito population ( Kidwell and Ribeiro, 1992 ). (nap.edu)
- Ends-out gene targeting (GT) supplies just such a method by allowing seamless replacement of endogenous sequences with engineered DNA fragments ( Thomas and Capecchi 1987 ). (genetics.org)
- One can therefore place designer "genes" into their native loci or otherwise edit the nucleotide sequences in any genomic region of interest. (genetics.org)
- These RNA sequences fold into specific three-dimensional shapes that act as molecular receptors for certain intracellular metabolites. (searlescholars.net)
- Our lab is interested in discovering just how often, and in what capacity, these interesting and important RNA sequences are utilized inside a given cell. (searlescholars.net)
- Hif1a gene target sequences are the same in both mice and humans, thereby the method presented in this study could be used in the future for the treatment of ADM in human patients. (eurekalert.org)
- S. cerevisiae RPB3 subunit from RNA polymerase II. (ebi.ac.uk)
- Schizosaccharomyces pombe rpb3 subunit from RNA polymerase II. (ebi.ac.uk)
- Archaebacterial RNA polymerase subunit D (gene rpoD). (ebi.ac.uk)
- The amino acid sequence of the human RNA polymerase II 33-kDa subunit hRPB 33 is highly conserved among eukaryotes. (ebi.ac.uk)
- Azuma Y, Yamagishi M, Ishihama A. Subunits of the Schizosaccharomyces pombe RNA polymerase II: enzyme purification and structure of the subunit 3 gene. (ebi.ac.uk)
- Bacterial sRNAs have a wide variety of regulatory mechanisms. (wikipedia.org)
- These long ncRNAs appear to be functioning as an endogenous RNA regulatory system, playing a major role in the epigenetic control of differentiation and development. (keystonesymposia.org)
- RNAs are also involved in modification of other nucleic acids, as unstructured regulatory oligonucleotides, and as structured trans-acting regulatory RNAs. (searlescholars.net)
- The recent implication of regulatory RNAs (small RNAs [sRNAs]) in antibiotic response and resistance in several bacterial pathogens suggests that they should be considered innovative drug targets. (asm.org)
- Retroviral and lentiviral vectors differ in their integration patterns with respect to genes and gene regulatory regions. (els.net)
- Our results suggest that under certain conditions, interpretation and modeling of natural and synthetic gene regulatory circuits need to take into account the spatial organization of the transcripts of participating genes. (weizmann.ac.il)
- Spatial Fluctuations in Expression of the Heterocyst Differentiation Regulatory Gene hetR in Anabaena Filaments. (weizmann.ac.il)
- RNA targeting with CRISPR-Cas13. (addgene.org)
- The template for this profile is stored in the bacteriums own genes, specifically in those regions scientists call CRISPR (which stands for clustered regularly interspaced small palindromic repeats or, more simply put, the regular arrangement of small, symmetric repeats in the sequence of the DNA building blocks). (infectioncontroltoday.com)
- Together, the enzyme and the profile RNA constitute the CRISPR-Cas system. (infectioncontroltoday.com)
- Knowing about these different versions is not only of academic interest but can also be tremendously useful for gene technology: The CRISPR-Cas system is capable of cleaving DNA at very specific sites, explains Charpentier. (infectioncontroltoday.com)
- A team of researchers at the Gene Editing Institute in Newark, Delaware, has successfully treated chemotherapy-resistant lung cancer cells with the CRISPR gene-editing technique. (asbestos.com)
- Using the CRISPR method, the team turned off the NRF2 gene in chemotherapy-resistant lung cancer cells. (asbestos.com)
- This approach is especially promising because CRISPR allows manipulation of genes with more accuracy and precision than previous methods. (asbestos.com)
- CRISPR also offers a way to treat cancer without altering human genes, which raises fewer ethical concerns. (asbestos.com)
- Thus, CRISPR /Cas9 is rapidly becoming the tool of choice for gene editing in plants, but further testing is needed to determine whether efficacy will be universal. (plantphysiol.org)
- To test the efficacy of CRISPR /Cas9 in tomato, we chose to target a gene that, when function was disrupted, would result in a distinctive, immediately recognizable phenotype early in the plant tissue culture phase of Agrobacterium tumefaciens -mediated transformation. (plantphysiol.org)
- CRISPR /Cas9-mediated gene editing in stable transgenic tomato plants. (plantphysiol.org)
- Nou, X. & Kadner, R. J. Adenosylcobalamin inhibits ribosome binding to btuB RNA. (nature.com)
- Evolutionary model for the bacterial ribosome. (nature.com)
- One of the most critical components of cells, the ribosome , is composed primarily of RNA. (wikipedia.org)
- A limited number of studies have been conducted to analyze ribosomal RNA (rRNA, present in the ribosome) in bioaerosol samples to identify currently or potentially active airborne microbes, although its genomic counterpart, the rRNA gene (on the chromosome) has been frequently targeted for airborne microbial community analysis. (cdc.gov)
- All the catalytic properties of the ribosome can be found within its rRNA, and of all ribosomal genes, these are the most conserved. (scienceblogs.com)
- Tomato-optimized isolation of nuclei tagged in specific cell types and translating ribosome affinity purification binary vectors were generated and used to monitor associated messenger RNA abundance or chromatin modification. (plantphysiol.org)
- Their cellular experiments confirmed that EZH2 binds to B2 RNA and, when subjected to heat, cuts or cleaves the RNA molecule. (phys.org)
- Knockdown of the insulator factor CCCTC binding factor (CTCF), which binds XL9 , an intergenic element located between HLA-DRB1 and HLA-DQA1 , was found to diminish expression of these genes. (rupress.org)
- Rho will then wrap the downstream RNA (the RNA between where Rho binds and the RNA polymerase) around itself and slowly pull itself to the RNA polymerase, which is now paused. (wikibooks.org)
- Promoters ( Pro ) of these genes were isolated and fused to the β - glucuronidase ( GUS ) reporter gene. (springer.com)
- The finM promoter and the traM promoter are the principal promoters of the traM gene of the antibiotic resistance plasmid R100. (biomedsearch.com)
- We verified that the traM and finM promoters provide virtually all the transcripts originating in the R100-1 traM gene. (biomedsearch.com)
- We further characterized novel sRNAs from typhus ( R. prowazekii and R. typhi ) and spotted fever ( R. rickettsii and R. conorii ) groups for their promoters and Rho-independent terminators using Bacterial Promoter Prediction Program (BPROM) and TransTermHP prediction algorithms, respectively. (biomedcentral.com)
- d) SIN transfer vector with two genes expressed in opposite directions from two promoters. (els.net)
- This is a computer graphic of an RNA molecule. (phys.org)
- A study from Massachusetts General Hospital (MGH) investigators has found a surprising role for what had been considered a nonfunctional "junk" RNA molecule: controlling the cellular response to stress. (phys.org)
- We have shown, for the first time, that EZH2 can act outside of the PRC2 complex to activate genes through another mechanism-in this case by cleaving the B2 RNA molecule, which then activates stress response genes. (phys.org)
- Future studies will investigate the specific mechanism by which EZH2 is attracted to stress genes and how it cleaves the B2 RNA molecule. (phys.org)
- In March 2020, astronomer Tomonori Totani presented a statistical approach for explaining how an initial active RNA molecule might have been produced randomly in the universe sometime since the Big Bang . (wikipedia.org)
- One version of the hypothesis is that a different type of nucleic acid , termed pre-RNA , was the first one to emerge as a self-reproducing molecule, to be replaced by RNA only later. (wikipedia.org)
- Single-cell and single-molecule studies demonstrated that noise within gene expression is influenced by a combination of both intrinsic and extrinsic factors. (biochemsoctrans.org)
- In this study we show that SV induces IFN-αβ gene expression normally in cells from mice with targeted deletions of the Toll-IL-1 resistance domain containing adapters MyD88, Mal, Toll/IL-1R domain-containing adaptor inducing IFN-β (TRIF), and TRIF-related adaptor molecule TLR3, or the E3 ubiquitin ligase, TNFR-associated factor 6. (jimmunol.org)
- Using single-molecule fluorescence in situ hybridization, we measured transcript numbers of the RyhB-regulated genes sodB and fumA in individual cells as a function of iron deprivation. (weizmann.ac.il)
- These structures refine the pathway from preinitiation through initiation to elongation for the RNA-dependent RNA polymerization reaction, explain the role of the noncatalytic divalent cation in 6 RdRp, and pinpoint the previously unresolved Mn(2+)-dependent step in replication. (rcsb.org)
- Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. (uniprot.org)
- A whole RNA silencing process comprises three stages: initiation, maintenance, and signal amplification. (frontiersin.org)
- Initiation: RNA polymerase will move along the DNA, looking for the -35 region and -10 region of the sigma-70 promoter in E.Coli. (wikibooks.org)
- The recent discovery that short hybrid RNA:DNA molecules (siHybrids) induce long-term silencing of gene expression in mammalian cells conflicts with the currently hypothesized mechanisms explaining the action of small, interfering RNA (siRNA). (unt.edu)
- We recently discovered a new noncoding RNA surveillance pathway in mammalian cells. (cancer.gov)
- While some is translated into RNA molecules required for maintaining and regulating cellular functions-such as transfer RNA and microRNAs - the impression that most noncoding RNA serves no function has persisted. (phys.org)
- Sequencing of RNA molecules, and their subsequent quantification, aims to assess global gene expression changes on the RNA level (transcriptome). (biomedcentral.com)
- PPA and BA induced broad alterations in gene expression including neurotransmitter systems, neuronal cell adhesion molecules, inflammation, oxidative stress, lipid metabolism and mitochondrial function, all of which have been implicated in ASD. (plos.org)
- they are 50- to 500-nucleotide non-coding RNA molecules, highly structured and containing several stem-loops. (wikipedia.org)
- The remaining genes provide instructions for making molecules called transfer RNA (tRNA) and ribosomal RNA (rRNA), which are chemical cousins of DNA. (medlineplus.gov)
- A recent genomewide search for genes encoding short nontranslated RNAs yielded 17 new sRNAs, many of which bind Hfq ( 8 ). (pnas.org)
- One of these newly discovered sRNAs, RyhB (encoded by the ryhB gene), was found to be complementary to a portion of the sdhCDAB operon encoding succinate dehydrogenase. (pnas.org)
- It is now known that most bacterial sRNAs are encoded by free-standing genes located in the intergenic regions (IGR) between two known genes. (wikipedia.org)
- Since these initial discoveries, over six thousand bacterial sRNAs have been identified, largely through RNA-sequencing experiments. (wikipedia.org)
- Some cis-acting sRNAs act as riboswitches, which have receptors for specific environmental or metabolic signals and activate or repress genes based on these signals. (wikipedia.org)
- Conversely, trans-encoded sRNAs interact with genes on separate loci. (wikipedia.org)
- Amongst the targets of sRNAs are a number of house-keeping genes. (wikipedia.org)
- Of interest is the lack of knowledge about sRNAs implicated in Gram-positive compared to Gram-negative bacterial resistance. (asm.org)
- In recent years, substantial progress has been made in understanding bacterial gene expression by sRNAs. (weizmann.ac.il)
- Soukup, G. A. & Breaker, R. R. Engineering precision RNA molecular switches. (nature.com)
- Measuring how gene expression changes in the course of an experiment assesses how an organism responds on a molecular level. (biomedcentral.com)
- This text then examines the molecular mechanism by which steroid hormones regulate specific gene expression. (elsevier.com)
- In the 1960s Craig, Hamilton, Curtis and the other early pioneers did not yet have the molecular tools to engineer "desirable" genes or to molecularly tie them to a biased mechanism of inheritance. (nap.edu)
- We are working to uncover the molecular details for the novel mechanism by which this cleavage event results in a change in gene expression. (searlescholars.net)
- We are characterizing this new RNA surveillance pathway in molecular detail and determining how the packaged RNAs contribute to retrovirus replication. (cancer.gov)
- Previously, bacterial diversity of the infected root canal system was determined by broad-range polymerase chain reaction followed by cloning and Sanger sequencing as well as molecular fingerprinting techniques such as denaturing gradient gel and terminal restriction fragment length polymorphism analysis [ 5 , 11 ]. (hindawi.com)
- The proposed RNA-seq normalization method, moose 2 , is a valuable alternative to existing methods, with two major advantages: (i) in silico prediction of invariant genes provides a list of potential reference genes for downstream analyses, and (ii) non-linear artefacts in RNA-seq data are handled adequately to minimize variations between replicates. (biomedcentral.com)
- However, because no method has existed to isolate bacterial RNA away from host cell RNA, the corresponding analyses of bacterial transcriptomes has been impossible. (bio-medicine.org)
- Finally, RNA-sequencing analyses suggest that the NTT and CD broadly activate gene expression, whereas the BL and SID activate or repress gene expression in a gene-dependent manner for a subset of mycobacterial genes. (asm.org)
- Thus, ribosomes have been shown to exhibit high functional modularity and interoperability in the bacterial translation system. (nature.com)
- According to the complexity hypothesis 9 , genes involved in complex biosystems, which are constrained by many interactions (as represented by ribosomes), tend to experience horizontal gene transfer (HGT) less frequently than those coding for products not involved in complex systems. (nature.com)
- Many antibiotics target bacterial ribosomes. (scienceblogs.com)
- RNA-seq indirectly measures the abundance of transcripts by the number of reads or fragments generated from a particular transcript. (biomedcentral.com)
- A central challenge in designing RNA-Seq-based experiments is estimating a priori the number of reads per sample needed to detect and quantify thousands of individual transcripts with a large dynamic range of abundance. (biomedcentral.com)
- Detection and quantification of low abundance transcripts by RNA-Seq can be enhanced in two main ways. (biomedcentral.com)
- Specifically, for experiments focused on comparing gene expression among various strains and/or growth conditions, the inclusion of more strains, timepoints, biological replicates, and/or growth conditions may be worth the tradeoff of lower depth per sample, as it may provide additional biological insights and/or statistical confidence that is more valuable than the ability to detect low abundance transcripts in each sample. (biomedcentral.com)
- The abundance of 16S rRNA in the outdoor air sample (1.3×106-4.9×107copies/m3) was about two orders of magnitude higher than that of 16S rRNA gene (6.9×103-1.5×105copies/m3). (cdc.gov)
- Soukup, G. A. & Breaker, R. R. Relationship between internucleotide linkage geometry and the stability of RNA. (nature.com)
- In Escherichia coli , the members of a major class of these RNAs act with the help of the RNA chaperone Hfq to regulate translation and/or stability of target mRNAs through base-pairing ( 1 - 4 ). (pnas.org)
- Nucleoside modifications are interesting due to their already known roles in translation fidelity, enzyme recognition, disease progression, and RNA stability. (mdpi.com)
- RNA Stability of RNA later -Treated Tissues After Multiple Freeze/Thaw Cycles. (thermofisher.com)
- Known Y. pseudotuberculosis virulence genes are transcriptionally regulated by temperature - most probably in order to adapt to the bacterium's life cycle outside and inside the host. (pubmedcentralcanada.ca)
- The mold-to-yeast transition is essential for virulence and is controlled by DRK1 , the dimorphism-regulating histidine kinase gene ( 14 ). (asm.org)
- Pro DIR16 and Pro OMT will enable functional gene analysis in monocots, and will facilitate engineering monocots for improved carbon metabolism, enhanced stress tolerance and bioenergy production. (springer.com)
- We experimentally verified the predictions of this method in the bacterium Escherichia coli , and show how moose 2 is able to (i) estimate the expression value distances between RNA-seq samples, (ii) reduce the variation of expression values across all samples, and (iii) to subsequently reveal new functional groups of genes during the late stages of DNA damage. (biomedcentral.com)
- Using this system, two putative membrane-bound DGCs from B. thuringiensis and Xanthomonas oryzae were verified to be functional by replacing pleD with the corresponding DGC genes. (nih.gov)
- Our results suggest that a major contributing factor to decreased expression levels in T7 based systems is chromosomal mutation resulting in loss of functional T7 RNA polymerase. (biomedcentral.com)
- SCFA are capable of altering host gene expression, partly due to their histone deacetylase inhibitor activity. (plos.org)
- Here, we identify a new mechanism of bacterial adaptation through broad suppression of RNA polymerase II-dependent (Pol II-dependent) host gene expression. (jci.org)
- These results suggest that by manipulating host gene expression, ABU strains promote tissue integrity while inhibiting pathology. (jci.org)
- Such bacterial modulation of host gene expression may be essential to sustain asymptomatic bacterial carriage by ensuring that potentially destructive immune activation will not occur. (jci.org)
- This TLR-independent induction of IFN-αβ after SV infection is replication dependent and mediated by the RNA helicase, retinoic acid-inducible gene-I (RIG-I) and not the related family member, melanoma differentiation-associated gene 5. (jimmunol.org)
- Many negative-strand RNA viruses replicate in the cytoplasm and are unlikely to expose structures produced during viral replication to TLRs (e.g., dsRNA, a product of viral replication). (jimmunol.org)
- A hallmark of retroviral replication is the stable maintenance of the transferred gene(s) during cell division. (els.net)
- The retroviral replication machinery leads to stable maintenance of a transferred gene. (els.net)
- Urinary tract infections (UTIs) constitute a highly relevant model of microbial adaptation in which some patients infected with Escherichia coli develop acute pyelonephritis, while other patients with bacteriuria exhibit an asymptomatic carrier state similar to bacterial commensalism. (jci.org)
- Rat liver total RNA (25 g) and E. coli total RNA (2 g) were mixed together and subjected to the MICROB Enrich procedure. (bio-medicine.org)
- MICROB Enrich was optimized using E. coli RNA in a background of human, mouse and rat RNA. (bio-medicine.org)
- Holliday junction resolvases encoded by homologous rusA genes in Escherichia coli K-12 and phage 82. (semanticscholar.org)