The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
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)
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.
Ribonucleic acid that makes up the genetic material of viruses.
A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
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)
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
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).
Viruses whose genetic material is RNA.
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 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 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 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.
The processes of RNA tertiary structure formation.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
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 molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.
A family of proteins that promote unwinding of RNA during splicing and translation.
Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.
The 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.
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 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 which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
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.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.
RNA present in neoplastic tissue.
An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3.
A 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.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. The enzyme functions in the nucleolar structure and transcribes DNA into RNA. It has different requirements for cations and salts than RNA polymerase II and III and is not inhibited by alpha-amanitin. EC 2.7.7.6.
RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.
Small kinetoplastid mitochondrial RNA that plays a major role in RNA EDITING. These molecules form perfect hybrids with edited mRNA sequences and possess nucleotide sequences at their 5'-ends that are complementary to the sequences of the mRNA's immediately downstream of the pre-edited regions.
Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.
Established cell cultures that have the potential to propagate indefinitely.
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).
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)
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).
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
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.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
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.
Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
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.
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.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
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.
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.
The rate dynamics in chemical or physical systems.
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.
Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).
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.
Complexes of RNA-binding proteins with ribonucleic acids (RNA).
Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.
The steps that generate the 3' ends of mature RNA molecules. For most mRNAs (RNA, MESSENGER), 3' end processing referred to as POLYADENYLATION includes the addition of POLY A.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
Short RNA, about 200 base pairs in length or shorter, that does not code for protein.
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.
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.
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.
Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
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.
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)
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.
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.
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.
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)
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.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.
Any 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.
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.
Ribonucleic acid in chloroplasts having regulatory and catalytic roles as well as involvement in protein synthesis.
Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
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)
Deoxyribonucleic acid that makes up the genetic material of viruses.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Viruses parasitic on plants higher than bacteria.
Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
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.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
A method of studying a drug or procedure in which both the subjects and investigators are kept unaware of who is actually getting which specific treatment.
Interruption or suppression of the expression of a gene at transcriptional or translational levels.
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.
Elements of limited time intervals, contributing to particular results or situations.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.
Proteins found in any species of bacterium.
A transfer RNA which is specific for carrying phenylalanine to sites on the ribosomes in preparation for protein synthesis.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Proteins prepared by recombinant DNA technology.
A transfer RNA which is specific for carrying lysine to sites on the ribosomes in preparation for protein synthesis.
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.
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.
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.
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
A 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.
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.
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.
The functional hereditary units of VIRUSES.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
A transfer RNA which is specific for carrying tyrosine to sites on the ribosomes in preparation for protein synthesis.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
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)
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.
The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.

Mammalian staufen is a double-stranded-RNA- and tubulin-binding protein which localizes to the rough endoplasmic reticulum. (1/2793)

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

RNA binding by the novel helical domain of the influenza virus NS1 protein requires its dimer structure and a small number of specific basic amino acids. (2/2793)

The RNA-binding/dimerization domain of the NS1 protein of influenza A virus (73 amino acids in length) exhibits a novel dimeric six-helical fold. It is not known how this domain binds to its specific RNA targets, one of which is double-stranded RNA. To elucidate the mode of RNA binding, we introduced single alanine replacements into the NS1 RNA-binding domain at specific positions in the three-dimensional structure. Our results indicate that the dimer structure is essential for RNA binding, because any alanine replacement that causes disruption of the dimer also leads to the loss of RNA-binding activity. Surprisingly, the arginine side chain at position 38, which is in the second helix of each monomer, is the only amino-acid side chain that is absolutely required only for RNA binding and not for dimerization, indicating that this side chain probably interacts directly with the RNA target. This interaction is primarily electrostatic, because replacement of this arginine with lysine had no effect on RNA binding. A second basic amino acid, the lysine at position 41, which is also in helix 2, makes a strong contribution to the affinity of binding. We conclude that helix 2 and helix 2', which are antiparallel and next to each other in the dimer conformation, constitute the interaction face between the NS1 RNA-binding domain and its RNA targets, and that the arginine side chain at position 38 and possibly the lysine side chain at position 41 in each of these antiparallel helices contact the phosphate backbone of the RNA target.  (+info)

Maturation, activation, and protection of dendritic cells induced by double-stranded RNA. (3/2793)

The initiation of an immune response is critically dependent on the activation of dendritic cells (DCs). This process is triggered by surface receptors specific for inflammatory cytokines or for conserved patterns characteristic of infectious agents. Here we show that human DCs are activated by influenza virus infection and by double-stranded (ds)RNA. This activation results not only in increased antigen presentation and T cell stimulatory capacity, but also in resistance to the cytopathic effect of the virus, mediated by the production of type I interferon, and upregulation of MxA. Because dsRNA stimulates both maturation and resistance, DCs can serve as altruistic antigen-presenting cells capable of sustaining viral antigen production while acquiring the capacity to trigger naive T cells and drive polarized T helper cell type 1 responses.  (+info)

Activation of target-tissue immune-recognition molecules by double-stranded polynucleotides. (4/2793)

Abnormal expression of major histocompatibility complex (MHC) class I and class II in various tissues is associated with autoimmune disease. Autoimmune responses can be triggered by viral infections or tissue injuries. We show that the ability of a virus or a tissue injury to increase MHC gene expression is duplicated by any fragment of double-stranded (ds) DNA or dsRNA introduced into the cytoplasm of nonimmune cells. Activation is sequence-independent, is induced by ds polynucleotides as small as 25 bp in length, and is not duplicated by single-stranded polynucleotides. In addition to causing abnormal MHC expression, the ds nucleic acids increase the expression of genes necessary for antigen processing and presentation: proteasome proteins (e.g., LMP2), transporters of antigen peptides; invariant chain, HLA-DM, and the costimulatory molecule B7.1. The mechanism is different from and additive to that of gamma-interferon (gammaIFN), i.e., ds polynucleotides increase class I much more than class II, whereas gammaIFN increases class II more than class I. The ds nucleic acids also induce or activate Stat1, Stat3, mitogen-activated protein kinase, NF-kappaB, the class II transactivator, RFX5, and the IFN regulatory factor 1 differently from gammaIFN. CpG residues are not responsible for this effect, and the action of the ds polynucleotides could be shown in a variety of cell types in addition to thyrocytes. We suggest that this phenomenon is a plausible mechanism that might explain how viral infection of tissues or tissue injury triggers autoimmune disease; it is potentially relevant to host immune responses induced during gene therapy.  (+info)

Molecular characterization of two endogenous double-stranded RNAs in rice and their inheritance by interspecific hybrids. (5/2793)

We completely sequenced 13,936 nucleotides (nt) of a double-stranded RNA (dsRNA) of wild rice (W-dsRNA). A single long open reading frame (13,719 nt) containing the conserved motifs of RNA-dependent RNA polymerase and RNA helicase was located in the coding strand. The identity between entire nucleotide sequence of W-dsRNA and that of the dsRNA of temperate japonica rice (J-dsRNA, 13,952 nt) was 75.5%. A site-specific discontinuity (nick) was identified at nt 1,197 from the 5' end of the coding strand of W-dsRNA. This nick is also located at nt 1,211 from the 5' end in the coding strand of J-dsRNA. The dsRNA copy number was increased more than 10-fold in pollen grains of both rice plants. This remarkable increase may be responsible for the highly efficient transmission of J-dsRNA via pollen that we already reported. J-dsRNA and W-dsRNA were also efficiently transmitted to interspecific F1 hybrids. Seed-mediated dsRNA transmission to F2 plants was also highly efficient when the maternal parent was wild rice. The efficiency of dsRNA transmission to F2 plants was reduced when the maternal parent was temperate japonica rice; however, the reduced rates in F2 plants were returned to high levels in F3 plants.  (+info)

Precise packaging of the three genomic segments of the double-stranded-RNA bacteriophage phi6. (6/2793)

Bacteriophage phi6 has a genome of three segments of double-stranded RNA. Each virus particle contains one each of the three segments. Packaging is effected by the acquisition, in a serially dependent manner, of the plus strands of the genomic segments into empty procapsids. The empty procapsids are compressed in shape and expand during packaging. The packaging program involves discrete steps that are determined by the amount of RNA inside the procapsid. The steps involve the exposure and concealment of binding sites on the outer surface of the procapsid for the plus strands of the three genomic segments. The plus strand of segment S can be packaged alone, while packaging of the plus strand of segment M depends upon prior packaging of S. Packaging of the plus strand of L depends upon the prior packaging of M. Minus-strand synthesis begins when the particle has a full complement of plus strands. Plus-strand synthesis commences upon the completion of minus-strand synthesis. All of the reactions of packaging, minus-strand synthesis, and plus-strand synthesis can be accomplished in vitro with isolated procapsids. Live-virus constructions that are in accord with the model have been prepared. Mutant virus with changes in the packaging program have been isolated and analyzed.  (+info)

The complete genome sequence of the major component of a mild citrus tristeza virus isolate. (7/2793)

The genome of the Spanish mild isolate T385 of citrus tristeza virus (CTV) was completely sequenced and compared with the genomes of the severe isolates T36 (Florida), VT (Israel) and SY568 (California). The genome of T385 was 19,259 nt in length, 37 nt shorter than the genome of T36, and 33 and 10 nt longer than those of VT and SY568, respectively, but their organization was identical. T385 had mean nucleotide identities of 81.3, 89.3 and 94% with T36, VT and SY568, respectively. The 3' UTR had over 97% identity in all isolates, whereas the 5' UTR of T385 had 67% identity with VT, 66.3% with SY568 and only 42.5% with T36. In the coding regions, the nucleotide differences between T385 and VT were evenly distributed along the genome (around 90% identity); this was not observed between T385 and the other isolates. T385 and T36 had nucleotide identities around 90% in the eight 3'-terminal ORFs of the genome, but only 72.3% in ORF 1a, a divergence pattern similar to that reported previously for T36 and VT. T385 and SY568 had nucleotide identities close to 90% in the 5'- and 3'-terminal regions of the genome, whereas the central region had over 99% identity. Our data suggest that the central region in the SY568 genome results from RNA recombination between two CTV genomes, one of which was almost identical to T385.  (+info)

New defective RNAs from citrus tristeza virus: evidence for a replicase-driven template switching mechanism in their generation. (8/2793)

Defective RNAs (D-RNAs) ranging in size from 1968 to 2759 nt were detected in four citrus tristeza virus (CTV) isolates by hybridization of electroblotted dsRNAs with two probes specific for the 5'- and 3'-terminal genomic regions. The RNAs that hybridized with both probes were eluted, cloned and sequenced. Comparison with the sequences of the corresponding genomic regions of the helper virus showed, in all cases, over 99% nucleotide identity and direct repeats of 4-5 nt flanking or in the vicinity of the junction sites. The presence of the repeats from two separate genome locations suggests a replicase-driven template switching mechanism for the generation of these CTV D-RNAs. Two of the CTV isolates that differed greatly in their pathogenicity contained an identical D-RNA, suggesting that it is unlikely that this D-RNA is involved in symptom modulation, which may be caused by another factor.  (+info)

Research in my laboratory is focused on double-stranded RNA (dsRNA)-its biologic functions and the proteins that bind it to mediate these functions. Our studies are divided between two dsRNA-mediated pathways: RNA editing by adenosine deaminases that act on RNA (ADARs), and gene-silencing (e.g., RNA interference). For both pathways we perform in vitro studies to answer mechanistic questions, and in vivo studies in C. elegans to understand biologic function. dsRNA binding proteins (dsRBPs) bind tightly to dsRNA of any sequence, and a dsRNA substrate for one dsRBP is also a substrate for others. Thus, dsRNA-mediated pathways intersect, and we also study how RNA editing affects dsRNA-mediated processes such as gene-silencing.ADARs deaminate adenosines in double-stranded regions of cellular and viral RNAs to create the nucleoside inosine. Several years ago my laboratory made the surprising discovery that the predominant site of editing by ADARs is not in codons, but in long double-stranded ...
Double-stranded (ds) RNA interference (RNAi) is widely used as a reverse genetic approach for functional analysis of plant genes. Constitutive or transient RNAi effects in plants have been achieved vi
In mammals, double-stranded RNA (dsRNA) can mediate sequence-specific RNA interference, activate sequence-independent interferon response, or undergo RNA editing by adenosine deaminases. dsRNA expression represents a hidden danger in transient transfection experiments and must be taken into account during interpretation of experimental results. Introduction Double-stranded RNA (dsRNA) is a unique structure with important biological effects. Viruses often give rise to dsRNA during their life cycle; therefore, dsRNA is recognized by a vertebrate cell as a hallmark of viral presence (reviewed in [1]). dsRNA can also arise endogenously in a cell, being formed upon basepairing between complementary transcripts or by intramolecular pairing within a transcript, thus forming a hairpin. In mammalian cells, dsRNA can enter three pathways: RNA interference (RNAi), RNA editing, and the interferon response. RNAi mediates sequence-specific RNA degradation guided by 22 nt small interfering RNAs (siRNAs) ...
RNAi is an RNA-dependent gene silencing process that is controlled by the RNA-induced silencing complex (RISC) and is initiated by short double-stranded RNA molecules in a cells cytoplasm, where they interact with the catalytic RISC component argonaute.[5] When the dsRNA is exogenous (coming from infection by a virus with an RNA genome or laboratory manipulations), the RNA is imported directly into the cytoplasm and cleaved to short fragments by Dicer. The initiating dsRNA can also be endogenous (originating in the cell), as in pre-microRNAs expressed from RNA-coding genes in the genome. The primary transcripts from such genes are first processed to form the characteristic stem-loop structure of pre-miRNA in the nucleus, then exported to the cytoplasm. Thus, the two dsRNA pathways, exogenous and endogenous, converge at the RISC.[6] Exogenous dsRNA initiates RNAi by activating the ribonuclease protein Dicer,[7] which binds and cleaves double-stranded RNAs (dsRNAs) in plants, or short hairpin ...
RNAi is an RNA-dependent gene silencing process that is controlled by the RNA-induced silencing complex (RISC) and is initiated by short double-stranded RNA molecules in a cells cytoplasm, where they interact with the catalytic RISC component argonaute.[5] When the dsRNA is exogenous (coming from infection by a virus with an RNA genome or laboratory manipulations), the RNA is imported directly into the cytoplasm and cleaved to short fragments by Dicer. The initiating dsRNA can also be endogenous (originating in the cell), as in pre-microRNAs expressed from RNA-coding genes in the genome. The primary transcripts from such genes are first processed to form the characteristic stem-loop structure of pre-miRNA in the nucleus, then exported to the cytoplasm. Thus, the two dsRNA pathways, exogenous and endogenous, converge at the RISC.[6]. Exogenous dsRNA initiates RNAi by activating the ribonuclease protein Dicer,[7] which binds and cleaves double-stranded RNAs (dsRNAs) in plants, or short hairpin ...
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Self-complementary RNA transcripts form a double-stranded RNA (dsRNA) that triggers a sequence-specific mRNA degradation, in a process known as RNA interference (RNAi), leading to gene silencing. In vascular plants, RNAi molecules trafficking occur between cells and systemically throughout the plant. RNAi signals can spread systemically throughout a plant, even across graft junctions from transgenic to non-transgenic stocks. There is also a great interest in applying RNAi to pathogenic fungi. Specific inhibition of gene expression by RNAi has been shown to be suitable for a multitude of phytopathogenic filamentous fungi. However, double-stranded (ds)RNA/small interfering (si)RNA silencing effect has not been observed in vivo. This study demonstrates for the first time the in vivo interference phenomenon in the pathogenic fungus Fusarium verticillioides, in which expression of an individual fungal transgene was specifically abolished by inoculating mycelial cells in transgenic tobacco plants engineered
The claims of the Tuschl II patents are directed to methods of preparing a particular type of double-stranded RNA molecule that can mediate RNAi, Saris wrote. The molecule has a 3 overhang, a sequence of nucleotides on one end of an RNA strand that hangs over the other RNA strand and make up a double-stranded RNA molecule ...
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The adenovirus VA1 RNA (VA1.), a 160-nucleotide (nt)- long RNA transcribed by RNA polymerase III, is efficiently exported from the nucleus to the cytoplasm of infected cells, where it antagonizes the interferon-induced antiviral defense system. We recently reported that nuclear export of VA1 is mediated by a cis-acting RNA export motif, called minihelix, that comprises a double-stranded stem (> 14 nt) with a base-paired 5′ end and a 3-8-nt protruding 3′ end. RNA export mediated by the minibelix motif is Ran-dependent, which indicates the involvement of a karyopherin-related factor (exportin) that remained to be determined. Here we show using microinjection in Xenopus laevis oocytes that VA1 is transported to the cytoplasm by exportin-5, a nuclear transport factor for double-stranded RNA binding proteins. Gel retardation assays revealed that exportin-5 directly interacts with VA1 RNA in a RanGTP-dependent manner. More generally, in vivo and in vitro competition experiments using various ...
Toll-like receptors recognize molecules associated with pathogens and initiate inflammatory responses. For example, Toll-like receptor 3 (TLR3) recognizes double-stranded RNA (dsRNA), an intermediate viral replication. The TLR3 ectodomain binds as a dimer to dsRNA, but the molecular basis for signaling remains unclear. Liu et al. now report the structure of a complex between two mouse TLR3 ectodomains and dsRNA. Two horseshoe-shaped TLR3-ectodomain monomers bind to opposite faces of the dsRNA through their N and C termini and dimerize through their C termini so that the N termini are at opposite ends of the linear dsRNA molecule. This dimerization mode could mediate signal transduction by facilitating dimerization of the receptor cytoplasmic domains.. L. Liu, I. Botos, Y. Wang, J. N. Leonard, J. Shiloach, D. M. Segal, D. R. Davies, Structural basis of Toll-like receptor 3 signaling with double-stranded RNA. Science 320, 379-381 (2008). [Abstract] [Full Text]. ...
1 Fire,A, Xu, S, Montgomery, MK, Kostas, SA, Driver, SE, and Mello, CC (1998). Potent and specific genetic interference by doublestranded RNA in Caenorhabditis elegans. Nature 391: 806-811. 2 Kennerdell, JR and Carthew, RW (1998). Use of dsRNAmediated genetic interference to demonstrate that frizzled and frizzled 2 act in the wingless pathway. Cell 95: 1017-1026. 3 Hammond, SM, Caudy,AA, Hannon, GJ (2001). Posttranscriptional Gene Silencing by Double-stranded RNA. Nature Rev Gen 2: 110-119. 4 Elbashir,SM,Harborth,J, Lendeckel,W,Yalcin,A,Weber,K, and Tuschl,T (2001).Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells.Nature 411:494-498.. 5 McManus, MT and Sharp, PA (2002). Gene silencing in mammals by small interfering RNAs. Nature Rev Genet 3:737-747. 6 Gonczy,P, Echeverri,C,Oegema, K, Coulson,A, Jones, SJ, Copley, RR, Duperon, J,Oegema,J, Brehm, M, Cassin, E, Hannak, E, Kirkham, M, Pichler, S, Flohrs, K, Goessen,A, Leidel, S,Alleaume,AM,Martin,C, Ozlu, N, ...
Takashima K., Oshiumi H., Takaki H., Matsumoto M., Seya T.. MDA5 is a cytoplasmic viral double-stranded RNA (dsRNA) sensor and triggers type I interferon (IFN) production. MDA5 assembles along viral dsRNA, leading to the formation of an MDA5 filament required for activating the MAVS adaptor. A recent study has revealed that PP1α and PP1γ phosphatases are responsible for dephosphorylating MDA5 and are essential for its activation. Here, we identified RIO kinase 3 (RIOK3) as a protein kinase that phosphorylates the MDA5 C-terminal region. RIOK3 knockout strongly enhanced type I IFN and IFN-inducible gene expression following measles virus infection. Conversely, the ectopic expression of RIOK3 or a phosphomimetic MDA5-S828D mutation attenuated MDA5-mediated signaling. Moreover, RIOK3-mediated MDA5 phosphorylation impaired MDA5 multimer formation, indicating that MDA5 C-terminal phosphorylation interferes with MDA5 filament formation and suppresses its signaling. Our data revealed a regulatory ...
In this study we report for the first time expression of Oct-6 in fibroblasts and macrophages. We show that Oct-6 is induced by IFNβ and IFNγ, but not by IL-6. Expression of Oct-6 in response to IFNβ occurs mainly via the canonical Jak/Stat signalling cascade and is dependent on the presence of Stat1 and to a lesser extent on Tyk2. Notably, we observed delayed and low levels of Oct-6 induction in the absence of Stat1 in response to high dose of exogenous IFNβ, suggesting that additional IFN activated factors can mediate Oct-6 induction. Oct-6 is also expressed during viral infection and after treatment with the synthetic dsRNA analogue poly(I:C), in both cases mediated by autocrine/paracrine IFNα/β signalling. Using ChIP technology, we show that Stat1 directly binds to the Oct-6 promoter at around 387 to 481 bp upstream of the transcription start site, a region containing three conserved Stat1 consensus binding sites (i.e. two GAS sites and one imperfect ISRE). The presence of GAS and ISRE ...
Elvira-Matelot E, Hachet M, Shamandi N, Comella P, Saez-Vasquez J, Zytnicki M, Vaucheret H. The Arabidopsis RTL2 is an RNASE THREE LIKE protein with one RNAseIII domain and two dsRNA-binding domains. Its transient over-expression in plants is known to enhance the production of exogenous siRNAs. Here the authors investigate its role in the production of endogenous siRNAs.. The ectopic expression of RTL2 stimulates the production of siRNAs from artificial and natural Inverted Repeats constructs. Both its domains are necessary for the RTL2-dependent production of siRNAs from dsRNAs. Contrarily, in other cases the over-expression of RTL2 reduces the production of siRNAs from dsRNAs. The opposite effect of RTL2 on dsRNA substrates likely depends on the structure and/or sequence of the dsRNAs.. Interestingly, the over-expression of RTL2 also stimulates the production of RNA molecules larger than 24 nts from artificial and natural Inverted Repeats constructs. The authors also demonstrate that RTL2 ...
Many species, across a wide phylogenetic range, respond to aberrant/foreign RNA by degrading endogenous mRNA in a sequence-specific manner (1). This phenomenon, broadly referred to as posttranscriptional gene silencing (PTGS), can be triggered by the introduction of double-stranded RNA (dsRNA) [RNA interference (RNAi)], transformation with sense transgenes (cosuppression/quelling), or viral infection (2). RNAi acts as a cellular defense against parasitic nucleic acids and provides a fortuitous technique for biologists to reduce or eliminate a gene activity (3). RNAi-like mechanisms are also involved in the production of small noncoding RNAs that control developmental timing (4, 5). A better understanding of RNAi may then shed light on genome defense and endogenous developmental pathways.. The molecular mechanisms underlying RNAi are beginning to be elucidated. dsRNA is processed into small double-stranded fragments of 21-25 nucleotides, called small interfering RNA (siRNA; refs. 6-8), by the ...
As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
The discovery of double-stranded RNA-mediated gene silencing has rapidly led to its use as a method of choice for blocking a gene, and has turned it into one of the most discussed topics in cell biology. Although still in its infancy, the field of RNA interference has already produced a vast array of results, mainly in Caenorhabditis elegans, but recently also in mammalian systems. Micro-RNAs are short hairpins of RNA capable of blocking translation, which are transcribed from genomic DNA and are implicated in several aspects from development to cell signaling. The present review discusses the main methods used for gene silencing in cell culture and animal models, including the selection of target sequences, delivery methods and strategies for a successful silencing. Expected developments are briefly discussed, ranging from reverse genetics to therapeutics. Thus, the development of the new paradigm of RNA-mediated gene silencing has produced two important advances: knowledge of a basic cellular ...
Staufen1 (STAU1)-mediated mRNA decay (SMD) degrades mammalian-cell mRNAs that bind the double-stranded RNA (dsRNA)-binding protein STAU1 in their 3 untranslated region. We report a new motif, which typifies STAU homologs from all vertebrate classes, that is responsible for human STAU1 (hSTAU1) homodimerization. Our crystal structure and mutagenesis analyses reveal that this motif, which we named the Staufen-swapping motif (SSM), and the dsRNA-binding domain 5 (RBD5) mediate protein dimerization: the two SSM alpha-helices of one molecule interact primarily through a hydrophobic patch with the two RBD5 alpha-helices of a second molecule. RBD5 adopts the canonical alpha-beta-beta-beta-alpha fold of a functional RBD, but it lacks residues and features required to bind duplex RNA. In cells, SSM-mediated hSTAU1 dimerization increases the efficiency of SMD by augmenting hSTAU1 binding to the ATP-dependent RNA helicase hUPF1. Dimerization regulates keratinocyte-mediated wound healing and many ...
CLAVEL M., PÉLISSIER T., MONTAVON T., TSCHOPP M.A., POUCH-PÉLISSIER M.N., DESCOMBIN J., JEAN V., DUNOYER P., BOUSQUET-ANTONELLI C. and DERAGON J.M.. Evolutionary history of double-stranded RNA binding proteins in plants: identification of new cofactors involved in easiRNA biogenesis. Plant Molecular Biology, 91(26858002):131-147, 2016. ...
We have demonstrated that NOSpro dsRNA can trigger methylation and transcriptional inactivation of homologous copies of the NOSpro in trans. In addition, this NOSpro dsRNA is degraded into small RNAs ∼23 nt in length, similar to the dsRNA degradation products observed with PTGS systems in plants (Hamilton and Baulcombe, 1999) and an RNAi in vitro system in Drosophila (Zamore et al., 2000). The production of these small RNAs indicates that at least some of the NOSpro dsRNA, which is synthesized in the nucleus, enters the same pathway as cytoplasmic dsRNAs involved in PTGS/RNAi. Therefore, the degradation process is not restricted to dsRNAs containing sequences that are normally transcribed (untranslated and coding regions) and targeted to mRNA. The similar fate of these dsRNAs strengthens the link between RNA‐mediated TGS and PTGS. dsRNA can trigger either the sequence‐specific RNA degradation step of PTGS/RNAi or DNA methylation, which can lead to TGS if promoter sequences are involved. ...
BACKGROUND: Ribosomal protein S7, a crucial RNA-binding component of the ribosome, is one of two proteins that initiates assembly of the 30S ribosomal subunit. It is required for proper folding of a large 3 domain of 16S ribosomal RNA. S7 regulates its own synthesis by binding to its own mRNA. This ability of S7 to bind both messenger and ribosomal RNAs makes determination of its mode of RNA recognition particularly interesting. RESULTS: The crystal structure of S7 from Thermus thermophilus was determined by a two-wavelength anomalous diffraction experiment using the LIII edge of mercury. The S7 structure consists of a bundle of six helices and an extended beta hairpin between helices 3 and 4, with two or more RNA-binding sites on its surface. The hairpin, along with portions of helices 1, 4 and 6, forms a large, positively charged, concave surface that has the appropriate curvature and dimensions to bind double-stranded RNA. A second putative RNA-binding site comprises parts of loop 2 and the ...
In vitro binds long double-stranded RNA (dsRNA) (500 and 700 base pairs), but not dsRNA shorter than 300 bp. Not involved in RNA autophagy, a process in which RNA is directly imported into lysosomes in an ATP-dependent manner, and degraded.
Click to launch & play an online audio visual presentation by Prof. Long-Cheng Li on Activation of gene expression by double-stranded RNAs, part of a collection of online lectures.
RNA interference (RNAi) is an evolutionarily conserved defence mechanism whereby genes are specifically silenced through degradation of messenger RNAs; this process is mediated by homologous double-stranded (ds)RNA molecules. In invertebrates, long dsRNAs have been used for genome-wide screens and have provided insights into gene functions. Because long dsRNA triggers a nonspecific interferon response in many vertebrates, short interfering (si)RNA or short hairpin (sh)RNAs must be used for these organisms to ensure specific gene silencing. Here we report the generation of a genome-scale library of endoribonuclease-prepared short interfering (esi)RNAs from a sequence-verified complementary DNA collection representing 15,497 human genes. We used 5,305 esiRNAs from this library to screen for genes required for cell division in HeLa cells. Using a primary high-throughput cell viability screen followed by a secondary high content videomicroscopy assay, we identified 37 genes required for cell ...
RNAi refers to dsRNA-induced gene silencing, a cellular process that degrades RNA homologous to one strand of the dsRNA [1, 2]. The intermediates of long dsRNA-initiated RNAi are double-stranded small interfering RNAs (siRNA), typically 21-23 nucleotide (nt) long. The siRNAs, when introduced into cells, can be used to silence genes in mammalian systems where long dsRNAs prompt protein kinase R (PKR), RNase L, and interferon activities that result in non-specific RNA degradation and general shutdown of protein synthesis [3]. siRNAs can either be chemically synthesized then directly transfected into cells or can be generated inside the cell by introducing vectors that express short-hairpin RNA (shRNA) precursors of siRNAs. The process of shRNA into functional siRNA involves cellular RNAi machinery that naturally process genome encoded microRNAs (miRNA) that are responsible for cellular regulation of gene expression by modulating mRNA stability, translation, and chromatin structures ...
RNA interference involves the targeted knockdown of mRNA triggered by complementary dsRNA molecules applied to an experimental organism. Although this technique has been successfully used in honeybees
Researchers from MIT have cobbled together a chimerical protein called DRACO that causes virus-infected cells to self destruct. Cell defenses already recognize long double-stranded RNA, a form of genetic material not normally produced in mammals, but which is a starting or intermediate step for mos...
In recent years, the recognition of non-protein coding RNAs as a functional effector of genetic expression has been highlighted by the discovery of RNA interference (RNAi). RNAi is an intracellular phenomenon that enables the eukaryotic cell to utilize double-stranded RNA molecules to silence gene expression in a sequence-specific manner. The short interfering RNA (siRNA) pathway has been intensively investigated and continues to serve as the basis for the development of potent molecular genetic tools. The power of this technology is most clearly evidenced by the fact that siRNA effector molecules can be chemically synthesized and exogenously delivered to specifically target and silence any gene of choice. This capability enables not only basic research, but also opens the door to a new therapeutic modality. Furthermore, the introduction of certain chemical modifications to siRNA effectors can produce a more robust knockdown of gene expression, hence, optimizing serum stability and increasing target
A process is provided of introducing an RNA into a living cell to inhibit gene expression of a target gene in that cell. The process may be practiced ex vivo or in vivo. The RNA has a region with double-stranded structure. Inhibition is sequence-specific in that the nucleotide sequences of the duplex region of the RNA and of a portion of the target gene are identical. The present invention is distinguished from prior art interference in gene expression by antisense or triple-strand methods.
Relevant publications in the last five years:. - D. Luque, J.R. Castón; Cryo-electron microscopy for the study of virus assembly; Nature Chemical Biology 2020, 16, 231.. - M.V. de Ruiter, R. Klem, D. Luque, J.J.L.M. Cornelissen, J.R. Castón; Structural nanotechnology: three-dimensional cryo-EM and its use in the development of nanoplatforms for in vitro catalysis Nanoscale 2019, 11, 4130.. - C.P. Mata, J. Mertens, J. Fontana, D. Luque, C. Allende-Ballestero, D. Reguera, B.L. Trus, A.C. Steven, J.L. Carrascosa, J.R. Castón; The RNA-binding protein of a double-stranded RNA virus acts like a scaffold protein; J. Virol. 2018, 92, e00968.. - C.P. Mata, D. Luque, J. Gómez-Blanco, J.M. Rodríguez, J.M. González, N. Suzuki, S.A. Ghabrial, J.L. Carrascosa, B.L. Trus, J.R. Castón; Acquisition of functions on the outer capsid surface during evolution of double-stranded RNA fungal viruses; PLOS Pathog. 2017, 13, e1006755.. - R.M. Putri, C. Allende-Ballestero, D. Luque, R. Klem, K.-A. Rousou, ...
Virus-induced gene silencing (VIGS) is a powerful reverse genetics technology used to unravel the functions of genes. It uses viruses as vectors to carry targeted plant genes. The virus vector is used to induce RNA-mediated silencing of a gene or genes in the host plant. The process of silencing is triggered by dsRNA molecules, the mechanism is explained in this chapter. Over the years a large number of viruses have been modified for use as VIGS vectors and a list of these vectors is also included. As the name suggests, virus-induced gene silencing uses the host plants natural defense mechanisms against viral infection to silence plant genes. VIGS is methodologically simple and is widely used to determine gene functions, including disease resistance, abiotic stress, biosynthesis of secondary metabolites and signal transduction pathways. Here, we made an attempt to describe the basic underlying molecular mechanism of VIGS, the methodology and various experimental requirements, as well as its ...
GO:0016246. The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation (silencing) both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes. ...
Authors: Yin, Cuifeng; Montelione, Gaetano. Citation: Yin, Cuifeng; Khan, Javed; Swapna, Gurla; Ertekin, Asli; Krug, Robert; Tong, Liang; Montelione, Gaetano. Conserved surface features form the double-stranded RNA binding site of non-structural protein 1 (NS1) from influenza A and B viruses. J. Biol. Chem. 282, 20584-20592 (2007).. Assembly members: ...
What happened? Was 21mer length optimal?. Their findings were quite unexpected: they observed that synthetic RNA duplexes 25-30 nucleotides in length could be up to 100-fold more potent than corresponding 21mer siRNAs. Why? The 27mers were later shown to be a substrate for Dicer, and were processed down to 21mer size. Drs. Rossi and Behlke theorize that increased potency may result from forcing the system to interact with Dicer, which then invokes a natural RISC loading pathway that is denied to 21mer RNAs. The 27mers primed the Dicer pump, resulting in better access of the 21mer product for RISC.. This meant that less siRNA would be needed for gene silencing - i.e., that the RNAs were more potent and could be used at lower dose. Important for many reasons among them less toxicity and lower research expense.. Please see: Dong Ho Kim, Mark Behlke, Scott Rose, Mi-Sook Chang, Sangdun Choi & John Rossi. Synthetic dsRNA Substrates Enhance SiRNA Potency and Efficacy Nature Biotechnology. Published ...
This patent search tool allows you not only to search the PCT database of about 2 million International Applications but also the worldwide patent collections. This search facility features: flexible search syntax; automatic word stemming and relevance ranking; as well as graphical results.
As part of the PANACEA (for Pharmacological Augmentation of Nonspecific Anti-pathogen Cellular Enzymes and Activities) project, researchers from MIT Lincoln Laboratory have developed and demonstrated a novel broad-spectrum antiviral approach, called DRACO (for Double-stranded RNA [dsRNA] Activated Caspase Oligomerizer). DRACO selectively induces apoptosis, or cell suicide, in cells containing any viral dsRNA, rapidly killing infected cells without harming uninfected cells. As a result, DRACO should be effective against virtually all viruses, rapidly terminating a viral infection while minimizing the impact on the patient ...
Double stranded nucleic acid is denatured by subjecting a solution thereof to a voltage applied between electrodes spaced by no more than 1.5 mm in a time not previously achievable in electrochemical denaturation. PCR is practiced isothermally by periodic application of voltage to produce denaturation. Electrochemical cells and kits for use in the process are provided.
DI-fusion, le Dépôt institutionnel numérique de lULB, est loutil de référencementde la production scientifique de lULB.Linterface de recherche DI-fusion permet de consulter les publications des chercheurs de lULB et les thèses qui y ont été défendues.
yes i am working with iRNA and i got a protocol to separate them, working with the supernatant of a simple RNA extraction,and after several steps with LiCl, ethanol and phenol-chlorophorm to wash it i can detect with a blot. But because dsRNA is not that easy to get this way, i need to process around 3 gr of roots and it is not always enough, without saying that i need to do several samples at the time. So, i was wondering if there is another way to do it. Maybe using some column ...
The possibility of blocking the expression of selected genes raises great hopes for the treatment of incurable diseases so far , such as neurodegenerative diseases , autoimmune diseases and cancer . The RNA molecule due to its biochemical properties of a promising therapeutic tool . The discovery of RNA interference (RNAi ) started the new tests for inhibition of expression of selected genes by small interfering RNA ( siRNA) in mammalian cells. This technique uses a natural process of gene silencing the expression of double-stranded RNA -dependent . ...
1. Viruses and other informational parasites are a fact of life 304. 2. Evolution drives diversity in viral strategies and host interactions 304. 3. Cellular defense often involves recognizing nucleic acid structures that are indicative of unwanted information duplication 305. 3.1 Double-stranded RNA (dsRNA) 305. 3.2 Single-stranded DNA (ssDNA) 305. 3.3 Unspliced mRNAs 306. 3.4 Polycistronic mRNAs 306. 3.5 Multi-copy DNAs 306. 3.6 Other structures 306. 4. dsRNA as a case study: building a multilevel response to foreign structure 306. 5. Getting there is half the fun: disseminated immunity in RNAi 308. 6. Viruses strike back … so why do we still get sick? 308. Cells face a constant struggle against unwanted instructions that arrive in the form of viruses and transposons. At the core of this battle are two issues: how can cellular machinery recognize certain informational molecules as unwanted and how can the cell use this recognition to effectively silence malicious genetic activity. While ...
Silence (as most others) has been mostly troubled by the Tuschl and Kreutzer-Limmer patents that make it very difficult for them to find dsRNA lengths to exploit their issued Atu-siRNA design pattern without having to to get a license from Alnylam: blunt-ended dsRNAs with alternate 2-O-methyl modified RNAs. Atu-027 for example, the combined companys lead candidate for solid cancers that has entered phase I studies this summer, is a 23bp dsRNA and Tuschl I should be a formidable challenge here. Intradigm, like RXi/Invitrogens non-Dicer dsRNAs before (rxRNA solo/Stealth), chose to minimize Tuschl-KL problems by opting for a 25bp blunt-end design, and Silences alternating 2-O-methylation pattern IP might give those a proprietary touch. As I cannot find any evidence that Intradigm currently has any access to 25bp structure-specific patents aside from Fire-Mello, I wonder how extensive the siRNA design IP access to the Zamore (University of Massachusetts) patent estate really is. Zamores ...
RNA interference (RNAi) is a way to block the production of any gene product. To produce this effect, all you have to do is to introduce double-stranded RNA that is complementary in sequence to your targted gene. RNAi was developed first in the worm C. elegans and there are many good web sites where you can learn more about the metod and what has been learned using RNAi. ...
Johnston further reported that the shRNAs were at least as efficient as the corresponding siRNAs with some of the IC50s in the low picomolar range. I am curious how this will translate into in vivo uses for example because shRNAs, unlike classical siRNAs and Rossi-type two-stranded Dicer-substrates, contain the double-stranded RNA within one molecule which should make this structure thermodynamically quite stable. A potential disadvantage is that it is so much more expensive to synthetically make the ~42-55 nucleotide hairpin RNAs since cost and purity of manufacturing RNAs increases more than linearly after you reach a certain size, say 25 nucleotides. While these studies mostly used RNAs generated through biochemical synthesis in the test tube using recombinant phage RNA polymerases, for the clinic they are working together with Agilent to generate the same RNAs to scale. I say the same here since the phage polymerase leaves a triphosphate 5 end while chemical synthesis does not. This is ...
Theodora Hatziioannou discusses a macaque model for AIDS, and how a cell protein that blocks HIV-1 infection interacts with double-stranded RNA.
The fact that coimmunoprecipitation of PKR with E3 was dependent on Lys-167 and Arg-168 in the E3 DRBM suggests that PKR resides in heteromeric complexes containing both E3 and dsRNA. This seems at odds with the dsRNA sequestration model, in which E3 prevents PKR from interacting with dsRNA, and more consistent with the notion that E3 inhibits PKR via heterocomplex formation. It could be argued that E3 and PKR do not directly interact with one another in these complexes but simply bind independently to the same dsRNA molecules. To explain our coimmunoprecipitation results by this hypothesis, the numbers of dsRNA and E3 molecules would have to be nearly equivalent in yeast cells. If dsRNA molecules were in large molar excess of E3, then PKR would most frequently bind to dsRNA molecules lacking E3. If E3 was in large molar excess of dsRNA, it would compete with PKR for limited dsRNA binding sites (as suggested by the dsRNA sequestration model). In either case, most of the PKR would not be ...
Semantic Scholar extracted view of The war against the interferon-induced dsRNA-activated protein kinase: can viruses win? by Michael G. Katze
Recently we reported that introduction of catalytically inactive PKR molecules into NIH 3T3 cells causes malignant transformation and the development of tumors in nude mice. We have proposed that PKR may be a tumor suppressor gene possibly because of its translational inhibitory properties. We have now designed and characterized a number of PKR mutants encoding proteins that retain their catalytic competence but are mutated in their regulatory double-stranded RNA (dsRNA) binding domains (RBDs). RNA binding analysis revealed that PKR proteins either lacking or with point mutations in the first RBD (RBD-1) bound negligible amounts of dsRNA activator or adenovirus VAI RNA inhibitor. Despite the lack of binding, such variants remained functionally competent but were much less active than wild-type PKR. PKR variants completely lacking RBD-1 were largely unresponsive to dsRNA in activation assays but could be activated by heparin. To complement these studies, we evaluated the effects of point ...
BACKGROUND: Inflammation may be involved in the pathogenesis of Alzheimers disease (AD). There has been little success with anti-inflammatory drugs in AD, while the promise of anti-inflammatory treatment is more evident in experimental models. A new anti-inflammatory strategy requires a better understanding of molecular mechanisms. Among the plethora of signaling pathways activated by β-amyloid (Aβ) peptides, the nuclear factor-kappa B (NF-κB) pathway could be an interesting target. In virus-infected cells, double-stranded RNA-dependent protein kinase (PKR) controls the NF-κB signaling pathway. It is well-known that PKR is activated in AD. This led us to study the effect of a specific inhibitor of PKR on the Aβ42-induced inflammatory response in primary mixed murine co-cultures, allowing interactions between neurons, astrocytes and microglia. METHODS: Primary mixed murine co-cultures were prepared in three steps: a primary culture of astrocytes and microglia for 14 days, then a primary ...
BACKGROUND: Inflammation may be involved in the pathogenesis of Alzheimers disease (AD). There has been little success with anti-inflammatory drugs in AD, while the promise of anti-inflammatory treatment is more evident in experimental models. A new anti-inflammatory strategy requires a better understanding of molecular mechanisms. Among the plethora of signaling pathways activated by β-amyloid (Aβ) peptides, the nuclear factor-kappa B (NF-κB) pathway could be an interesting target. In virus-infected cells, double-stranded RNA-dependent protein kinase (PKR) controls the NF-κB signaling pathway. It is well-known that PKR is activated in AD. This led us to study the effect of a specific inhibitor of PKR on the Aβ42-induced inflammatory response in primary mixed murine co-cultures, allowing interactions between neurons, astrocytes and microglia. METHODS: Primary mixed murine co-cultures were prepared in three steps: a primary culture of astrocytes and microglia for 14 days, then a primary culture of
TY - JOUR. T1 - Mast cells contribute to double-stranded RNA-induced augmentation of airway eosinophilia in a murine model of asthma. AU - Kan-o, Keiko. AU - Matsunaga, Yuko. AU - Fukuyama, Satoru. AU - Moriwaki, Atsushi. AU - Hirai-Kitajima, Hiroko. AU - Yokomizo, Takehiko. AU - Aritake, Kosuke. AU - Urade, Yoshihiro. AU - Nakanishi, Yoichi. AU - Inoue, Hiromasa. AU - Matsumoto, Koichiro. N1 - Copyright: Copyright 2013 Elsevier B.V., All rights reserved.. PY - 2013/3/4. Y1 - 2013/3/4. N2 - Background: Clinical studies showed the contribution of viral infection to the development of asthma. Although mast cells have multiple roles in the pathogenesis of allergic asthma, their role of in the virus-associated pathogenesis of asthma remains unknown. Most respiratory viruses generate double-stranded (ds) RNA during their replication. dsRNA provokes innate immune responses. We recently showed that an administration of polyinocinic polycytidilic acid (poly IC), a mimetic of viral dsRNA, during allergen ...
Biochemical data from many laboratories have clearly defined PKR as an IFN-inducible gene product whose enzymatic activity is stimulated by dsRNA (2, 10, 20, 27). Because of these properties, PKR has been predicted to play a major role in IFN-mediated antiviral defense. Indeed, PKR demonstrated an antiviral role in cultured cells following various means of overexpression of the wild type or catalytically inactive mutants (21, 22, 28). However, previous studies from our lab and others have failed to demonstrate a definitive role for PKR on an organismal level following genetic ablation of PKR in mice (1, 36). Yang et al. (36) challenged their PKR−/− mice with EMCV (∼1,000 PFU i.v.) and found no difference in survival from that of wild-type animals, but the mice did show a diminished protective effect from pretreatment with either IFN-γ or the dsRNA analogue poly(I · C). In a recent report, Zhou et al. have also shown only a very slight difference in survival between wild-type animals and ...
TY - JOUR. T1 - Alternaria inhibits double-stranded RNA-induced cytokine production through toll-like receptor 3. AU - Wada, Kota. AU - Kobayashi, Takao. AU - Matsuwaki, Yoshinori. AU - Moriyama, Hiroshi. AU - Kita, Hirohito. PY - 2013/4/12. Y1 - 2013/4/12. N2 - Background: Fungi may be involved in asthma and chronic rhinosinusitis (CRS). Peripheral blood mononuclear cells from CRS patients produce interleukin (IL)-5, IL-13 and interferon (IFN)-γ in the presence of Alternaria. In addition, Alternaria produces potent Th2-like adjuvant effects in the airway. Therefore, we hypothesized that Alternaria may inhibit Th1-type defense mechanisms against virus infection. Methods: Dendritic cells (DCs) were generated from mouse bone marrow. The functional responses were assessed by expression of cell surface molecules by FACS (MHC class II, CD40, CD80, CD86 and OX40L). Production of IL-6, chemokine CXCL10 (IP-10), chemokine CXCL11 (I-TAC) and IFN-β was measured by ELISA. Toll-like receptor 3 (TLR3) mRNA ...
Protein kinase RNA-activated also known as protein kinase R (PKR), interferon-induced, double-stranded RNA-activated protein kinase, or eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) is an enzyme that in humans is encoded by the EIF2AK2 gene. PKR protects against viral infections. Protein kinase-R is activated by double-stranded RNA (dsRNA), introduced to the cells by a viral infection. PKR can also be activated by the protein PACT or by heparin. PKR contains an N-terminal dsRNA binding domain (dsRBD) and a C-terminal kinase domain, that gives it pro-apoptotic (cell-killing) functions. The dsRBD consists of two tandem copies of a conserved double stranded RNA binding motif, dsRBM1 and dsRBM2. PKR is induced by interferon in a latent state. Binding to dsRNA is believed to activate PKR by inducing dimerization and subsequent auto-phosphorylation reactions. In situations of viral infection, the dsRNA created by viral replication and gene expression binds to the N-terminal ...
RNA interference (RNAi), a gene-silencing mechanism that involves providing double-stranded RNA molecules that match a specific target gene sequence, is now widely used in functional genetic studies. The potential application of RNAi-mediated control of agricultural insect pests has rapidly become evident. The production of transgenic plants expressing dsRNA molecules that target essential insect genes could provide a means of specific gene silencing in larvae that feed on these plants, resulting in larval phenotypes that range from loss of appetite to death. In this report, we show that the tomato leafminer (Tuta absoluta), a major threat to commercial tomato production, can be targeted by RNAi. We selected two target genes (Vacuolar ATPase-A and Arginine kinase) based on the RNAi response reported for these genes in other pest species. In view of the lack of an artificial diet for T. absoluta, we used two approaches to deliver dsRNA into tomato leaflets. The first approach was based on the uptake of
Receptor-mediated detection of pathogen-derived nucleic acids assists in protecting the host genome from invading foreign genetic material. Retinoic acid-inducible protein I (RIG-I) recognizes a specific set of RNA viruses (Flaviviridae, Paramyxoviridae, Orthomyxoviridae, and Rhabdoviridae) (1-3), whereas a second member of this protein family, melanoma differentiation-associated gene 5 (MDA-5), is responsible for the antiviral defense against a reciprocal set of RNA viruses (Picornaviridae) (3). The four members of the Toll-like receptor (TLR) family (TLR3, TLR7, TLR8, and TLR9) involved in viral nucleic acid recognition are located in the endosomal membrane. TLRs are largely dispensable for effective antiviral defense, whereas the two cytosolic helicases MDA-5 and RIG-I (1) are essential for controlling viral infection.. The molecular characteristic of double-strandedness seems to allow for the distinction of self and nonself RNA. In the endosome, long double-stranded RNA (dsRNA) and its ...
Cellular innate immune sensors detect foreign signals emanating from pathogens. Nallagatla et al. report that the pivotal sensing protein, double-stranded RNA-activated protein kinase (PKR), is finely tuned to recognize the 5′-triphosphate structures of single-stranded RNA molecules present in many bacteria and viruses. This recognition strategy is similar to the recently described detection of nucleic acid 5′-end signatures by another sensing protein, RIG-I. It remains unclear exactly how these key sensors go on to tailor the most appropriate cellular responses to intracellular pathogens.. S. R. Nallagatla, J. Hwang, R. Toroney, X. Zheng, C. E. Cameron, P. C. Bevilacqua, 5′-triphosphate-dependent activation of PKR by RNAs with short stem-loops. Science 318, 1455-1458 (2007). [Abstract] [Full Text]. ...
Characterizing the genome of mature virions is pivotal to understanding the highly dynamic processes of virus assembly and infection. Owing to the different cellular fates of DNA and RNA, the life cycles of double-stranded (ds)DNA and dsRNA viruses are dissimilar. In terms of nucleic acid packing, dsDNA viruses, which lack genome segmentation and intra-capsid transcriptional machinery, predominantly display single-spooled genome organizations1-8. Because the release of dsRNA into the cytoplasm triggers host defence mechanisms9, dsRNA viruses retain their genomes within a core particle that contains the enzymes required for RNA replication and transcription10-12. The genomes of dsRNA viruses vary greatly in the degree of segmentation. In members of the Reoviridae family, genomes consist of 10-12 segments and exhibit a non-spooled arrangement mediated by RNA-dependent RNA polymerases11-14. However, whether this arrangement is a general feature of dsRNA viruses remains unknown. Here, using cryo-electron
Recent studies have demonstrated that TLR3 forms dimeric complexes with 45-bp segments of dsRNA, and that single TLR3 dimers formed with a 48-bp dsRNA ON are capable of activating transfected cells expressing high amounts of TLR3 (27). A goal of this study was to determine how TLR3/dsRNA complexes, formed with dsRNA ONs of varying lengths, function in primary cells, and to translate these findings into the development of well-defined, TLR3-dependent adjuvants. In this study, we examined the activation of DC by dsRNA ONs because this response is key for inducing acquired antiviral immunity. We have previously shown that the interaction of TLR3-ECD protein with dsRNA is highly dependent on dsRNA length and TLR3-ECD concentration (27), which implies that the ability of a specifically sized dsRNA ON to bind TLR3 and activate a cell is governed, in part, by the membrane density of TLR3 in the endosomes. Thus, the large differences in TLR3 expression levels that we observed between DC subsets are ...
Double-stranded RNA triggers various profound cellular reactions, which depend not only on different intracellular dsRNA locations, but also on the intrinsic structure and length of the duplex. One of the major cellular responses to nuclear dsRNA is the covalent base modification of the target dsRNA by a ubiquitously expressed enzyme, ADAR. ADAR works on dsRNA and alters adenosines to inosines in the RNA duplex. Two types of ADAR editing of dsRNA have been found, selective editing and the promiscuous hyperediting. Hyperedited RNA has been suggested to undergo a novel regulatory pathway. How do cells discriminate between selectively edited mRNAs that encode new protein isoforms, and dsRNA-induced, promiscuously edited RNAs that encode nonfunctional, mutant proteins? We have developed a Xenopus oocyte model system which shows that a variety of hyperedited, inosine-containing RNAs are specifically retained in the nucleus. To uncover the mechanism of inosine-induced retention, HeLa cell nuclear extracts
This study identifies PKR as an essential mediator for several forms of stress-induced apoptosis. Specifically, our results implicate PKR in a signaling pathway that is responsive not only to dsRNA, but also to TNF-α and LPS. While the activation of PKR by dsRNA has been well studied (8), the mechanism of activation by these other stimuli is presently unclear. One possibility could involve the phosphorylation of PKR by an upstream kinase that is activated by one of the above stimuli [for example, the TNF-receptor-associated kinase, RIP (27), or a TNF-α/LPS-activated MAP kinase (4)]. Regardless of the activation mechanisms involved, our data show that PKR is required for regulating the DNA-binding ability of IRF-1 in response to stress-related stimuli. Previous studies have suggested that expression of IRF-1 protein in cells is insufficient to manifest any functional activity unless a phosphorylation signal is provided, potentially by PKR (28). While the mechanistic details of the interaction ...
Members of the RNase III family are the primary cellular agents of dsRNA (double-stranded RNA) processing. Bacterial RNases III function as homodimers and contain two dsRBDs (dsRNA-binding domains) and two catalytic sites. The potential for functional cross-talk between the catalytic sites and the requirement for both dsRBDs for processing activity are not known. It is shown that an Escherichia coli RNase III heterodimer that contains a single functional wt (wild-type) catalytic site and an inactive catalytic site (RNase III[E117A/wt]) cleaves a substrate with a single scissile bond with a k cat value that is one-half that of wt RNase III, but exhibits an unaltered K m . Moreover, RNase III[E117A/wt] cleavage of a substrate containing two scissile bonds generates singly cleaved intermediates that are only slowly cleaved at the remaining phosphodiester linkage, and in a manner that is sensitive to excess unlabelled substrate. These results demonstrate the equal probability, during a single ...
We describe a new method that allows cloning of double-stranded RNAs (dsRNAs) that are generated in RNase protection experiments. We demonstrate that the mouse C/D box snoRNA MBII-85 (SNORD116) is processed into at least five shorter RNAs using processing sites near known functional elements of C/D box snoRNAs. Surprisingly, the majority of cloned RNAs from RNase protection experiments were derived from endogenous cellular RNA, indicating widespread antisense expression. The cloned dsRNAs could be mapped to genome areas that show RNA expression on both DNA strands and partially overlapped with experimentally determined argonaute-binding sites. The data suggest a conserved processing pattern for some C/D box snoRNAs and abundant expression of longer, non-coding RNAs in the cell that can potentially form dsRNAs.
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RNase L and Ire1p are members of a superfamily of regulated endoribonucleases that play essential roles in mediating diverse types of cellular stress responses. 2′-5′ oligoadenylates, produced in response to interferon treatment and viral double-stranded RNA, are necessary to activate RNase L. In contrast, unfolded proteins in the endoplasmic reticulum activate Ire1p, a transmembrane serine/threonine kinase and endoribonuclease. To probe their similarities and differences, molecular properties of wild-type and mutant forms of human RNase L and yeast Ire1p were compared. Surprisingly, RNase L and Ire1p showed mutually exclusive RNA substrate specificity and partially overlapping but not identical requirements for phylogenetically conserved amino acid residues in their nuclease domains. A functional model for RNase L was generated based on the comparative analysis with Ire1p that assigns novel roles for ankyrin repeats and kinase-like domains.. ...
In 2010, a large study, which included all children born in Denmark between 1980 and 2005, highlighted an association between women who suffered an infection severe enough to require hospitalization while pregnant, and the presence of autism spectrum disorder (ASD) in their offspring: mothers who experienced a viral infection in the first trimester, or a bacterial infection in the second trimester, were much more likely to have a child with ASD. This phenomenon can be modeled in pregnant mice subjected to immune activation with specific antigens.. Now, results from a study recently (February 26, 2016) published in the journal Science (The maternal interleukin-17a pathway in mice promotes autismlike phenotypes in offspring) reveal a possible mechanism at the basis of the previous observations. The researchers injected pregnant mice with synthetic double-stranded RNA, a mimic of viral infection that induces severe inflammation. They found that the induced inflammatory response in the mother ...
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
Gene product distribution is often used to infer developmental similarities and differences in animals with evolutionarily diverse body plans. However, to address commonalties of developmental mechanisms, what is really needed is a method to assess and compare gene function in divergent organisms. This requires mutations eliminating gene function. Such mutations are often difficult to obtain, even in organisms amenable to genetic analysis. To address this issue we have investigated the use of double-stranded RNA interference to phenocopy null mutations. We show that RNA interference can be used to phenocopy mutations of the Deformed orthologues in Drosophila and Tribolium. We discuss the possible use of this technique for comparisons of developmental mechanisms in organisms with differing ontogenies. ...
As part of the InvaProtect project, we are investigating the hibernation of D. suzukii in our region, e.g. population dynamics, overwintering places and cold tolerance. The number of overwintered flies and the population build-up in spring are decisive factors for further infestation in cherries and berries. In a Biochance project, we aim to develop an alternative, environmentally friendly method for this control in springtime. It is based on the so-called RNA interference (RNAi) by application of small double-stranded RNAs, which are specific to D. suzukii, and thus have no effect on other (beneficial) insects. The RNA molecules are to be offered as food in an attractive trap. The control is based on a specific attract & kill strategy ...
a Royal Society of Chemistry journal, suggests this new approach could be key to addressing the threat to food security posed by plant pests, which account for a 40 per cent loss in global agricultural production and costs $100 billion every year. Professor Mark Dickman, from the Institute for Sustainable Food and Director of Research at the University of Sheffields Department of Chemical and Biological Engineering, led the study. He said: The RNA biocontrols we are working on with Syngenta can help to address the sustainability challenge for farming. The idea is that dsRNA is applied to the crops, then along comes the pest, which eats the crop. The dsRNA molecule then kills the pest by triggering the RNAi mechanism. The advantage of this is that we can be highly selective. We have the ability to target a specific pest while protecting beneficial species, such as honeybees. A key challenge will be making enough of these biocontrols which are natural, biodegradable and sustainable, and to ...
Although germinally transmitted ΔMuDR elements are transcriptionally active and produce chimeric sense/antisense transcripts, they have no measurable impact on mudrA transcript levels or Mu1 TIR methylation. As determined by in situ hybridization, antisense mudrA transcripts colocalized with sense mudrA and mudrB transcripts in many tissues of active Mutator plants, and the sense and antisense transcripts may have been paired in vivo (Joanin et al., 1997).. As with documented cases of quelling in fungi, RNA interference in animals, and cosuppression in transgenic plants (reviewed by Matzke et al., 2001; Vance and Vaucheret, 2001), structural properties of ΔMuDR transcripts would be predicted to lead to RNA-based epigenetic gene silencing (Walbot and Rudenko, 2002). Ectopically expressed antisense RNAs are thought to pair with sense transcripts and feed into the double-stranded RNA-induced degradation pathway (Stam et al., 2000; Van Houdt et al., 2000; Serio et al., 2001), and in such cases, ...
It is perhaps modern imaging technologies that have had the biggest impact on the field of cell biology, and will unquestionably continue to do so. The trend is to label and monitor cells, organelles and molecules and their interactions, using increasingly sophisticated tools, in real time. Not a meeting goes by without someone presenting a movie of their favourite protein dashing around a cell (sometimes even screened along with matching music), and these images are beginning to change our views of the dynamic nature of some of the most fundamental cell biological processes (see, for example, page 156 of this issue).. Because of the importance of technical advances across subdisciplines, Nature Cell Biology has recently introduced a new section, comprising Technology Review articles, which has so far included reviews of in vivo electroporation (Nature Cell Biol.1, E203-E207; 1999) and double-stranded RNA interference (RNAi) (Nature Cell Biol.2, E31-E36; 2000). This section is dedicated to ...
RNA activation (RNAa) is a small RNA-guided and Argonaute (Ago)-dependent gene regulation phenomenon in which promoter-targeted short double-stranded RNAs (dsRNAs) induce target gene expression at the transcriptional/epigenetic level. RNAa was first reported in a 2006 PNAS paper by Li et al. who also coined the term RNAa as a contrast to RNA interference (RNAi) to describe such gene activation phenomenon. Soon after, several groups made similar observation in different mammalian species including human, non-human primates, rat and mice, suggesting that RNAa is a general gene regulation mechanism conserved at least in mammals. In these studies, upregulation of gene expression is achieved by targeting selected promoter regions using either synthetic 21-nucleotide dsRNAs or vector expressed small hairpin RNAs (shRNAs). Such promoter targeted dsRNAs have been termed antigene RNA (agRNAs) or small activating RNA (saRNA). Similar gene activation mechanisms mediated by the Ago-small RNA pathway have ...
The absence of an alternatively spliced exon between the two dsRBMs of dADAR in adult flies results in higher editing activity when compared to the isoform containing the exon seen at earlier stages of development. A number of constructs containing the dsRBMs were successfully cloned and purified. NMR data of RBM1 confirms that the dsRBMs of dADAR are members of the well characterised family of dsRBMs. Each dsRBM has a distinct affinity for dsRNA substrate indicating possible different roles. Point mutations within dsRBM1 result in a loss of binding activity. The self editing site of dADAR is found within exon 7 of the pre-mRNA, 3 to the second catalytic motif of the deaminase domain. Editing at this site results in a serine to glycine change in the translated protein and has been shown to reduce editing activity in all known substrates. This region of the protein is highly conserved throughout the ADARs and sequence comparisons with human ADAR2 at the DNA level show it has the potential to be ...
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Increasingly complex networks of small RNAs act through RNA-interference (RNAi) pathways to regulate gene expression, to mediate antiviral responses, to organize chromosomal domains, and to restrain the spread of selfish genetic elements. Historically, RNAi has been defined as a response to double-stranded RNA. However, some small RNA species may not arise from double-stranded RNA precursors. Yet, like microRNAs and small interfering RNAs, such species guide Argonaute proteins to silencing targets through complementary base-pairing. Silencing can be achieved by corecruitment of accessory factors or through the activity of Argonaute itself, which often has endonucleolytic activity. As a specific and adaptive regulatory system, RNAi is used throughout eukarya, which indicates a long evolutionary history. A likely function of RNAi throughout that history is to protect the genome from both pathogenic and parasitic invaders.. ...
p,Intracellular RIG-I-like receptors (RLRs, including RIG-I, MDA-5, and LGP2) recognize viral RNAs as pathogen-associated molecular patterns (PAMPs) and initiate an antiviral immune response. To understand the molecular basis of this process, we determined the crystal structure of RIG-I in complex with double-stranded RNA (dsRNA). The dsRNA is sheathed within a network of protein domains that include a conserved helicase domain (regions HEL1 and HEL2), a specialized insertion domain (HEL2i), and a C-terminal regulatory domain (CTD). A V-shaped pincer connects HEL2 and the CTD by gripping an α-helical shaft that extends from HEL1. In this way, the pincer coordinates functions of all the domains and couples RNA binding with ATP hydrolysis. RIG-I falls within the Dicer-RIG-I clade of the superfamily 2 helicases, and this structure reveals complex interplay between motor domains, accessory mechanical domains, and RNA that has implications for understanding the nanomechanical function of this ...
Recognition of 5 triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus ...
Supervisor: Prof. Dr. Sven-Erik Behrens Specific aim/topic (1) Exploring the roles of TBSV P19 and TCV P38 in affecting antiviral and cellular RNA silencing. Background and significance. Small RNA-mediated RNA silencing is the primary adaptive immune response against (+)RNA viruses in higher plants. Inductors are structured elements of the viral genome or double-stranded RNAs that are generated by cellular RNA polymerases or during viral replication via (-)RNA intermediates. The RNA triggers are processed by the Dicers DCL2, 3 and 4 into 21-24 nt long vsiRNAs, which move ahead of the infection in the plant and may establish antiviral RNA silencing and immunity. As a key-feature of silencing, vsiRNAs are incorporated into RNA-induced silencing complexes (RISC) that contain ARGONAUTE (AGO) nucleases and other, yet uncharacterized components. Ten AGO proteins were identified in A. thaliana, from which AGO1, 2, 3, 5 and 7 were indicated to contribute to antiviral protection (see previous studies). ...
Currently there are relatively few antiviral therapeutics, and most which do exist are highly pathogen-specific or have other disadvantages. We have developed a new broad-spectrum antiviral approach, dubbed Double-stranded RNA (dsRNA) Activated Caspase Oligomerizer (DRACO) that selectively induces apoptosis in cells containing viral dsRNA, rapidly killing infected cells without harming uninfected cells. We have created DRACOs and shown that they are nontoxic in 11 mammalian cell types and effective against 15 different viruses, including dengue flavivirus, Amapari and Tacaribe arenaviruses, Guama bunyavirus, and H1N1 influenza. We have also demonstrated that DRACOs can rescue mice challenged with H1N1 influenza. DRACOs have the potential to be effective therapeutics or prophylactics for numerous clinical and priority viruses, due to the broad-spectrum sensitivity of the dsRNA detection domain, the potent activity of the apoptosis induction domain, and the novel direct linkage between the two which
In plants, many dsRNA-binding protein (DRBs) have already been proven to play essential roles in a variety of RNA silencing pathways, mainly by promoting the efficiency and/or accuracy of Dicer-like protein (DCL)-mediated little RNA production. also provides multiple lines of proof displaying that DRB4 is normally partitioned into, at least, two distinctive cellular pools satisfying different functions, through exceptional binding with either DCL4 or DRB7 mutually.2. Collectively, these results revealed that plant life have evolved a particular DRB complicated that modulates selectively the creation of endoIR-siRNAs. The life of such a complicated and its own implication about the still elusive natural function of place endoIR-siRNA will end up being discussed. Launch In eukaryotes, RNA silencing is normally a conserved system that plays important roles in lots of natural processes such as for example maintenance of genome balance, advancement or antiviral protection. The many classes of ...
CureVac, a German biotech that specializes in mRNA therapies has recently secured $110 million in fresh funding from new investors Chartwave Ltd., Coppel Family, Elma Investments Ltd. and Sigma Group as well as existing investors dievini Hopp BioTech holding GmbH & Co. KG and the Bill & Melinda Gates Foundation. Instead of using RNA for genetic interference, CureVac…
Small pieces of synthetic RNA trigger a RNA interference (RNAi) response that holds great therapeutic potential to treat a number of diseases, especially cancer and pandemic viruses. The problem is delivery - it is extremely difficult to get RNAi drugs inside the cells in which they are needed. To overcome this hurdle, researchers at University of California, San Diego School of Medicine have developed a way to chemically disguise RNAi drugs so that they are able to enter cells. Once inside, cellular machinery converts these disguised drug precursors - called siRNNs - into active RNAi drugs. The technique will publish Nov. 17 in Nature Biotechnology.
Introduction. The success of the Human Genome Project and the availability of the complete sequence of the human genome have revealed the existence of numerous genes whose functions are unknown. Although many functional genes were successfully identified using libraries of randomized ribozymes (Kruger et al., 2000; Li et al., 2000; Welch et al., 2000; Beger et al., 2001; Kawasaki et al., 2002; Kawasaki and Taira, 2002; Onuki et al., 2002; Nelson et al., 2003; Rhoades and Wong-Staal, 2003; Suyama et al., 2003a, b; Chatterton et al., 2004; Kuwabara et al., 2004; Onuki et al., 2004), the randomized library naturally contained many ribozymes that could not hybridize with any human gene transcripts, resulting in some false positives. While exploitation of RNA interference (RNAi) is hampered by the induction of the interferon response upon the introduction of double-stranded RNA (dsRNA) into mammalian cells (Elbashir et al., 2001), RNAi can be a powerful tool in gene analysis and, for example, the ...
One type of RNA editing involves the conversion of adenosine residues into inosine in double-stranded RNA (dsRNA) through the action of adenosine deaminase acti...
Our immune system has immense powers of observation. It needs to in order to fend off the millions of bacteria, viruses, fungi, you name it, that we get exposed to every day.. Im not talking about antibodies and T cells-parts of the immune systems adaptive arm, which is fine-tuned to recognize a specific virus or bacterium. Rather, Im talking about pattern recognition proteins-biological sensors capable of recognizing features and structures that only bacteria or viruses have. These make up the immune systems innate arm, which essentially primes the body to attack anything that looks remotely like it doesnt belong.. For instance, our cells carry sensors that can detect double-stranded RNA (dsRNA), which certain kinds of viruses use to encode their genome-like the rotavirus, which causes severe diarrhea in infants and small children. Our genome, by contrast, is encoded in DNA, and the RNA we make is single-stranded; if theres dsRNA present, it means theres a virus around.. In a recent ...
RNA interference is a specific inhibition of gene expression induced by the presence of a complementary double-stranded RNA, namely siRNA, in the cytoplasm. This silencing mechanism is present in plants, worms and mammalian cells, and is highly efficient and gene specific.
Ribonuclease R (RNase R) from E. coli, is a magnesium-dependent 3→5 exoribonuclease that digests essentially all linear RNAs but does not digest lariat or circular RNA structures1,2, or double-stranded RNA with 3 overhangs shorter than 7 nucleotides2
Typically a sign of viral infection, double-stranded RNAs were spotted in C9ORF72 carriers, in whom they mingled with cytoplasmic TDP-43 inclusions. In mice, dsRNAs spread between connected neurons, provoking Type I interferon response and killing cells. ...
Dicer-substrate short interfering RNAs (DsiRNAs) are chemically synthesized 27mer duplex RNAs that have increased potency compared to 21mer siRNAs.
Double-stranded RNA genome: Reoviridae. The Hepatitis D virus has not yet been assigned to a family, but is clearly distinct ... Partly double-stranded DNA viruses: Hepadnaviridae. These viruses are enveloped. One family of single-stranded DNA viruses ... Double-stranded DNA families: three are non-enveloped (Adenoviridae, Papillomaviridae and Polyomaviridae) and two are enveloped ... Positive single-stranded RNA families: three non-enveloped (Astroviridae, Caliciviridae and Picornaviridae) and four enveloped ...
Class VII: Double-stranded DNA with RNA intermediate. The genome of these viruses are gapped, double-stranded, and subsequently ... Class IV: Single-stranded RNA - Positive-sense. The genome of these viruses are positive-sense RNAs, in which the RNA is ... Class V: Single-stranded RNA - Negative-sense. All viruses in this class have negative-sense RNAs, in which the RNA complements ... Class III: Double-stranded RNA. The viruses in this class have segmented genomes. Each segment is transcribed individually to ...
Its ligand is retroviral double-stranded RNA (dsRNA), which activates the TRIF dependent signalling pathway. To explore the ... double-stranded RNA of viruses; or the unmethylated CpG islands of bacterial and viral DNA; and also of the CpG islands found ... TLR7 messenger RNA expression levels in dairy animals in a natural outbreak of foot-and-mouth disease have been reported. When ... in the promoters of eukaryotic DNA; as well as certain other RNA and DNA molecules. For most of the TLRs, ligand recognition ...
... double-stranded RNA viruses; (IV) positive-sense single-stranded RNA viruses; (V) negative-sense single-stranded RNA viruses; ( ... double-stranded DNA viruses that replicate through a single-stranded RNA intermediate. The greatest share of bat-associated ... double-stranded DNA viruses; (II) single-stranded DNA viruses; (III) ... VI) positive-sense single-stranded RNA viruses that replicate through a DNA intermediate; and (VII) ...
Example with double-stranded DNA[edit]. DNA strand 1: antisense strand (transcribed to) → RNA strand (sense). DNA strand 2: ... The "Watson strand" refers to 5′-to-3′ top strand (5′→3′), whereas the "Crick strand" refers to the 5′-to-3′ bottom strand (3′← ... it can recruit RNase H to degrade the target RNA. This makes the mechanism of gene silencing catalytic. Double-stranded RNA can ... one strand of the DNA serves as a template for the synthesis of a complementary strand of RNA. The transcribed DNA strand is ...
Such viruses are either single stranded RNA (e.g. HIV) or double stranded DNA (e.g. Hepatitis B virus) viruses. ... reverse transcriptase creates a complementary strand of DNA from the retrovirus RNA and the RNA is degraded; this strand of DNA ... RNA: consists of a dimer RNA. It has a cap at the 5' end and a poly(A) tail at the 3' end. The RNA genome also has terminal ... There are two strands of RNA within the cell that have three enzymes: protease, reverse transcriptase, and integrase (1). The ...
It is a double-stranded RNA virus. It is fusogenic and syncytia-forming. It varies from Nelson Bay virus in the S1 and S2 ... Double-stranded RNA viruses Oncolytic virus Orphan virus Xi River virus Cell-cell fusogens Pritchard LI, Chua KB, Cummins D, ...
A double-stranded RNA-binding protein and substrate for the double-stranded RNA-dependent protein kinase, PKR". Biochemistry. ... A double-stranded RNA-binding protein and substrate for the double-stranded RNA-dependent protein kinase, PKR". Biochemistry. ... C5orf36 Small NF90/ILF3-associated RNAs (snaR) (~120 nucleotides long) and are known to interact with ILF3 double-stranded RNA- ... Patel RC, Vestal DJ, Xu Z, Bandyopadhyay S, Guo W, Erme SM, Williams BR, Sen GC (July 1999). "DRBP76, a double-stranded RNA- ...
Many double stranded RNA elements that have been described in fungi do not fit this description, and in these cases they are ... The majority of mycoviruses have double-stranded RNA (dsRNA) genomes and isometric particles, but approximately 30% have ... The majority of mycoviruses have double-stranded RNA (dsRNA) genomes and isometric particles, but approximately 30% have ... Deng, F.; Xu, R.; Boland, G. J. (2003). "Hypovirulence-Associated Double-Stranded RNA from Sclerotinia homoeocarpa Is ...
... a double-stranded RNA binding protein. (DGCR8 is the name used in mammalian genetics, abbreviated from "DiGeorge syndrome ... DGCR8 recognizes the junctions between hairpin structures and single-stranded RNA and serves to orient Drosha to cleave around ... Michlewski G, Cáceres JF (January 2019). "Post-transcriptional control of miRNA biogenesis". RNA. 25 (1): 1-16. doi:10.1261/rna ... RNA. 22 (2): 175-83. doi:10.1261/rna.054684.115. PMC 4712668. PMID 26683315. Nguyen TA, Jo MH, Choi YG, Park J, Kwon SC, Hohng ...
... double-stranded RNA virus. The genome is segmented. Circoviruses are small single-stranded DNA viruses. There are to genera: ... It is a non-enveloped, positive strand, RNA virus. FMDV is a highly contagious virus. It enters the body through inhalation. ... African swine fever virus (ASFV) is a large double-stranded DNA virus which replicates in the cytoplasm of infected cells and ... Rhabdoviruses are a diverse family of single stranded, negative sense RNA viruses that infect a wide range of hosts, from ...
Replication follows the double-stranded RNA virus replication model. Double-stranded RNA virus transcription is the method of ... Genomes are linear double-stranded RNA which is around 12.5 kbp in length. The genome codes for four proteins. The genome has ... Alphachrysovirus is a genus of double-stranded RNA viruses. It is one of two genera in the family Chrysoviridae. They infect ... three double stranded RNA segments. All have extended highly conserved terminal sequences at both ends. Viral replication is ...
When, for example, double-stranded RNA molecules from an RNA viral infection bind to TLR-3 receptors, the virus in this way ... It is an immunomodulatory double-stranded RNA drug similar to the prototypical RNA poly I:C, first synthesized in the 1970s and ... "Mismatched Double-Stranded RNA: Ampligen, Oragen, Polyi:Polyc12u." Drugs in R&D. February 1, 2002. Retrieved on February 26, ... Rintatolimod development evolved from a 1960s synthesis by Merck & Co., a double-stranded RNA compound of inosinic and ...
"Ribonuclease III mechanisms of double-stranded RNA cleavage". Wiley Interdisciplinary Reviews: RNA. 5 (1): 31-48. doi:10.1002/ ... Inada, T.; Nakamura, Y. (1995). "Lethal double-stranded RNA processing activity of ribonuclease III in the absence of SuhB ... They process precursors to ribosomal RNA, small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA) Yeast nucleases with the ... They process precursors to ribosomal RNA, small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). The basic dsRNA cleavage ...
... where small interfering RNAs are produced from double-stranded RNA in order to create a sequence specific degradation pathway ... Hammond, Scott M.; Caudy, Amy A.; Hannon, Gregory J. (Feb 2001). "Post-transcriptional gene silencing by double-stranded RNA". ... The bacteria creates a mechanism that burrows a hole and transfers the new T-DNA strand into the plant cell. The T-DNA moves ... Although it is not clear exactly how p19 works to suppress RNA silencing, studies have shown that transiently expressed ...
DOUBLE-STRANDED-RNA VIRUS IN COLLETOTRICHUM-LINDEMUTHIANUM. Transactions of the British Mycological Society 65, no. oct, ( ... uniformly sized particles that he identified as double-stranded RNA viruses in the extract of the α5 race of fungus. The α5 ...
XRV has the same morphology and high sequence identity as Nelson Bay virus (NBV), and a 10-segmented double-stranded RNA genome ... Reoviruses are non-enveloped, double-stranded RNA viruses. They have an icosahedral capsid (T-13) composed of an outer and ... Patton JT (editor). (2008). Segmented Double-stranded RNA Viruses: Structure and Molecular Biology. www.horizonpress.com. ... Bat-borne virus Double-stranded RNA viruses Nelson Bay virus Oncolytic virus Orphan virus Du, L; Lu, Z; Fan, Y; Meng, K; Jiang ...
Replication follows the double-stranded RNA virus replication model. Double-stranded RNA virus transcription is the method of ... The genome is made of double-stranded RNA. It is linear and has twelve segments. Viral replication is cytoplasmic. Entry into ... Cardoreovirus is a genus of double-stranded RNA viruses in the family Reoviridae and subfamily Sedoreovirinae. Crabs serve as ...
Its genome is composed of segmented double-stranded RNA (dsRNA), thus it is classified as a group III virus according to the ... protein λ3 serves as the RNA-dependent RNA polymerase, full strands of positive sense single stranded RNA (mRNA) are ... positive sense RNAs serve as the template strand to make negative sense RNA. The positive and negative strands will base-pair ... Double-stranded RNA viruses Avian reovirus "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". ...
subscription required) Ngô, H.; Tschudi, C.; Gull, K.; Ullu, E. (1998). "Double-stranded RNA induces mRNA degradation in ...
Replication follows the double-stranded RNA virus replication model. Double-stranded RNA virus transcription is the method of ...
Replication follows the double-stranded RNA virus replication model. Double-stranded rna virus transcription is the method of ... "Intermediates in the assembly pathway of the double-stranded RNA virus phi6". EMBO J. 16 (14): 4477-87. doi:10.1093/emboj/16.14 ... Nucleotide Sequence of the Large Double-Stranded RNA". Virology. 295 (2): 266-271. doi:10.1006/viro.2002.1436. PMID 12033785. ... "Isolation of additional bacteriophages with genomes of segmented double-stranded RNA". J. Bacteriol. 181 (15): 4505-8. PMC ...
Replication follows the double-stranded RNA virus replication model. Double-stranded RNA virus transcription is the method of ... The genome is composed of a monopartite, linear double-stranded RNA molecule of 4.6-6.7 kilobases. It contains two overlapping ... Totiviridae is a family of double-stranded RNA viruses. Giardia lamblia, leishmania, trichomonas vaginalis, and fungi serve as ... Viruses in the family Totiviridae are non-enveloped, double-stranded RNA viruses with icosahedral geometries, and T=2 symmetry ...
Replication follows the double-stranded RNA virus replication model. Double-stranded RNA virus transcription is the method of ... Oryzavirus is a genus of double-stranded RNA viruses in the family Reoviridae and subfamily Spinareovirinae. Member viruses ...
Double-stranded RNA viruses Oncolytic virus Orphan virus "Viral Zone". ExPASy. Retrieved 15 June 2015. Guglielmi, KM; Johnson, ... 2008). Segmented Double-stranded RNA Viruses: Structure and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-21-9. ... Reoviridae is a family of double-stranded RNA viruses. Member viruses have a wide host range, including vertebrates, ... double-stranded RNA (dsRNA). Because of this, replication occurs exclusively in the cytoplasm, and the virus encodes several ...
... is a family of double-stranded RNA viruses. Members of the family are called chrysoviruses. The capsid is about ...
Replication follows the double-stranded RNA virus replication model. Double-stranded RNA virus transcription is the method of ... minitans RNA virus Eimeria brunetti RNA virus 1 Eimeria tenella RNA virus 1 Epichloe festucae virus 1 Gremmeniella abietina RNA ... Translation takes place by RNA termination-reinitiation. The virus exits the host cell by cell to cell movement. Filamentous ... virus 1 Magnaporthe oryzae virus 2 Rosellinia necatrix victorivirus 1 Sphaeropsis sapinea RNA virus 1 Sphaeropsis sapinea RNA ...
... es have twelve segments of linear, double-stranded RNA. When the genome is processed with gel electrophoresis, the ... DNA viruses have genomes consisting of deoxyribonucleic acid (or DNA), while RNA viruses, like Coltivirus, have an RNA ( ... Reassortment of the RNA segments in progeny is common, and this plays a role in some of the genetic diversity between the ... When the virus replicates, the virion outer shell has to be removed in order for RNA polymerase to be activated to continue the ...
Liu, W; Chen, J (2009). "A double-stranded RNA as the genome of a potential virus infecting Vicia faba". Virus Genes. 39 (1): ... Amalgaviridae is a family of double-stranded RNA viruses. Member viruses infect plants and are transmitted vertically via seeds ... been suggested that amalgaviruses have evolved via recombination between viruses with double-stranded and negative-strand RNA ... viruses of the Amalgaviridae family evolved via recombination between viruses with double-stranded and negative-strand RNA ...
3 RNA-Viren *3.1 Doppelsträngige RNA-Viren (dsRNA, double stranded RNA). *3.2 Einzelstrang-RNA-Viren mit negativer Polarität ( ... Doppelsträngige RNA-Viren (dsRNA, double stranded RNA)[Bearbeiten , Quelltext bearbeiten]. Viren mit Doppelstrang-RNA-Genom ... ss(−)RNA: negative single-stranded RNA). *3.3 Einzelstrang-RNA-Viren mit positiver Polarität (ss(+)RNA: positive single ... Einzelstrang-RNA-Viren mit negativer Polarität (ss(−)RNA: negative single-stranded RNA)[Bearbeiten , Quelltext bearbeiten]. ...
RNA editing in plastidsEdit. RNA editing is the insertion, deletion, and substitution of nucleotides in a mRNA transcript prior ... Segments with labels on the inside reside on the B strand of DNA, segments with labels on the outside are on the A strand. ... The results of the microscopy experiments led to the idea that chloroplast DNA replicates using a double displacement loop (D- ... When replication forks form, the strand not being copied is single stranded, and thus at risk for A → G deamination. Therefore ...
Coleoids rely mostly on ADAR enzymes for RNA editing, which requires large double-stranded RNA structures to flank to the ... RNA editing. Octopuses and other coleoid cephalopods are capable of greater RNA editing (which involves changes to the nucleic ... High levels of RNA editing do not appear to be present in more basal cephalopods or other molluscs.[118][119] ... More than 60% of RNA transcripts for coleoid brains are recoded by editing, compared to less than 1% for a human or fruit fly. ...
In biology, a probe is a single strand of DNA or RNA that is complementary to a nucleotide sequence of interest. ... This variation is often called double-fusion FISH or D-FISH. In the opposite situation-where the absence of the secondary color ... Single-molecule RNA FISH[edit]. Single-molecule RNA FISH, also known as Stellaris® RNA FISH,[11] is a method of detecting and ... doi:10.1261/rna.2701111. PMC 3096040. PMID 21518807.. *^ a b c Bernasconi, B.; Karamitopolou-Diamantiis, E.; Tornillo, L.; ...
double-stranded DNA binding. • single-stranded DNA-dependent ATPase activity. Cellular component. • cytoplasm. • site of double ... messenger RNA. [13]. Breast cancer (progesteron receptor negative). Over-expression. -. messenger RNA. [16]. ... In double-strand break repair[edit]. Double-strand break (DSB) repair by homologous recombination is initiated by 5' to 3' ... replication-born double-strand break repair via sister chromatid exchange. • cellular response to DNA damage stimulus. • strand ...
... strand RNA genome is replicated through a double-stranded RNA intermediate that is formed using viral RDRP (RNA-Dependent RNA ... The mRNA encodes RNA dependent RNA polymerase. This polymerase makes complementary minus strands of RNA, then uses them as ... Genomic RNAs of picornaviruses possess multiple RNA elements and they are required for both negative and plus strand RNA ... Virus RNA polymerases use VPg as primer. VPg as primer uses both minus and plus strand RNA synthesis. Picornavirus replication ...
... can be infected by double-stranded DNA viruses that are unrelated to any other form of virus and have a variety of ... Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular RNA ... although there are many introns in their transfer RNA and ribosomal RNA genes,[146] and introns may occur in a few protein- ... Werner F (September 2007). "Structure and function of archaeal RNA polymerases". Mol. Microbiol. 65 (6): 1395-404. doi:10.1111/ ...
... where it is initiated by recruitment of the RNA-induced transcriptional silencing (RITS) complex to double stranded RNAs ... Phosphorylated H2AX (also known as gamma H2AX) is a marker for DNA double strand breaks,[82] and forms part of the response to ... Bekker-Jensen S, Mailand N (Dec 2010). "Assembly and function of DNA double-strand break repair foci in mammalian cells". DNA ... Rogakou EP, Pilch DR, Orr AH, Ivanova VS, Bonner WM (Mar 1998). "DNA double-stranded breaks induce histone H2AX phosphorylation ...
"Use of two-dimensional NMR in the study of a double-stranded DNA". J. Am. Chem. Soc. 104 (20): 5540-5541. doi:10.1021/ ... such as DNA or RNA. It is useful for molecules of up to 100 nucleotides, and as of 2003, nearly half of all known RNA ... The first NMR spectrum of a double-helical DNA was published in 1977[9] using a synthetic, 30-base-pair double helix. To ... because errors add up as the double helix is traversed, and unlike with proteins, the double helix does not have a compact ...
... gene silencing by double-stranded RNA"[۷۹] ۲۰۱۱ بروس بویتلر ایالات متحده آمریکا به خاطر «اکتشافات فعال‌سازی سیستم ایمنی ذاتی ... "for their discovery of catalytic properties of RNA"[۳۳] ۱۹۹۲ رادولف مارکوس[۱] United States "for his contributions to the ...
double-stranded DNA binding. · sequence-specific DNA binding transcription factor activity. · sequence-specific enhancer ... binding RNA polymerase II transcription factor activity. · transcription factor binding. · zinc ion binding. · DNA bending ...
Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans". Nature 391: 806-11 ... RNA interference (z angl., česky doslova „rušení RNA"), zkratka RNAi, je relativně nedávno objasněný proces, kterým je ... Animace znázorňující RNA-interfernci z nakladatelství NATURE REVIEWS. *Objev RNA Interference (vyžaduje Flash), z Howard Hughes ... V tomto článku byl použit překlad textu z článku RNA interference na anglické Wikipedii. ...
... to denature the double-stranded DNA. The denaturation in an alkaline environment may improve binding of the negatively charged ... In some cases, the hybridization probe may be made from RNA, rather than DNA. To ensure the specificity of the binding of the ... Restriction endonucleases are used to cut high-molecular-weight DNA strands into smaller fragments. ... but using RNA or protein, have later been named in reference to Edwin Southern's name. As the label is eponymous, Southern is ...
The overall structure of RNA and DNA are immensely similar-one strand of DNA and one of RNA can bind to form a double helical ... a strand of RNA that would make creating more strands of RNA easier). Relatively short RNA molecules with such abilities have ... and an RNA polymerase ribozyme can synthesize a short RNA strand from a primed RNA template.[27] ... Atkins JF, Gesteland RF, Cech T (2006). The RNA world: the nature of modern RNA suggests a prebiotic RNA world. Plainview, N.Y ...
Toll-like receptors are located in the endosomal membrane and recognize double-stranded RNA (dsRNA), MDA5 and RIG-I receptors ... RNA silencing mechanisms are also important in the plant systemic response, as they can block virus replication.[40] The ... Baulcombe D (September 2004). "RNA silencing in plants". Nature. 431 (7006): 356-63. Bibcode:2004Natur.431..356B. doi:10.1038/ ... For example, the Influenza A virus produces NS1 protein, which can bind to host and viral RNA, interact with immune signaling ...
RNA, ((2'-deoxy-2'-fluoro)C-Gm-Gm-A-A-(2'-deoxy-2'-fluoro)U-(2'-deoxy-2'-fluoro)C-Am-Gm-(2'-deoxy-2'-fluoro)U-Gm-Am-Am-(2'- ... Pegaptanib is a pegylated anti-vascular endothelial growth factor (VEGF) aptamer, a single strand of nucleic acid that binds ... double-blind randomized clinical studies that lasted for approximately two years each. For this study approximately 1200 ...
... detecting single stranded RNA. Following activation of the toll-like receptor, intracellular signaling cascades are initiated, ... which forms a double membrane known as an autophagosome, around the organelle marked for destruction.[28][31] The autophagosome ... targeted cytoplasmic constituents are isolated from the rest of the cell within a double-membraned vesicle known as an ... "Subversion of cellular autophagosomal machinery by RNA viruses". PLoS Biol. 3 (5): e156. doi:10.1371/journal.pbio.0030156. PMC ...
5% are double stranded RNA and so can be immediately translated as +ssRNA viruses. 3% require a reverse transcriptase enzyme to ... the rest of the genome producing negative strand sub-genomic RNAs then act upon these to form positive strand sub-genomic RNAs ... 75% of plant viruses have genomes that consist of single stranded RNA (ssRNA). 65% of plant viruses have +ssRNA, meaning that ... Instead, the naked viral RNA may alter the function of the cells through a mechanism similar to RNA interference, in which the ...
Integration occurs following production of the double-stranded viral DNA by the viral RNA/DNA-dependent DNA polymerase reverse ... the strand transfer reaction, in which the processed 3' ends of the viral DNA are covalently ligated to the host chromosomal ... Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P (March 2010). "Retroviral intasome assembly and inhibition of DNA strand ... double-blind, phase 3 trial, analysis of results after 48 weeks". Lancet. 379 (9835): 2439-48. doi:10.1016/S0140-6736(12)60917- ...
... single-stranded RNA), dsRNA (double-stranded RNA), ssDNA (single-stranded DNA), or dsDNA (double-stranded DNA). It may be ... RNA is physically different from DNA: DNA contains two intercoiled strands, but RNA only contains one single strand. RNA also ... They are transfer RNA (tRNA) and ribosomal RNA (rRNA).. tRNA[change , change source]. Transfer RNA (tRNA) is a short molecule ... Protein synthesis RNAs[change , change source]. Messenger RNA[change , change source]. The structure of a mature eukaryotic ...
RNA tends to be single stranded but in special cases it is double.[64] Unusually for a virus, its genome is not a single piece ... Because of the absence of RNA proofreading enzymes, the RNA-dependent RNA polymerase that copies the viral genome makes an ... The viral RNA (vRNA) molecules, accessory proteins and RNA-dependent RNA polymerase are then released into the cytoplasm (Stage ... These core proteins and vRNA form a complex that is transported into the cell nucleus, where the RNA-dependent RNA polymerase ...
... or by formation of double-stranded RNA (RNAi). Descendants of the cell in which the gene was turned on will inherit this ... "Double strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG ... 5-Methylcytosine performs much like a regular cytosine, pairing with a guanine in double-stranded DNA. However, some areas of ... a double strand break in DNA can initiate unprogrammed epigenetic gene silencing both by causing DNA methylation as well as by ...
Anti-double stranded DNA (anti-dsDNA) antibodies are highly associated with SLE. They are a very specific marker for the ... 54kDa and 60kDa proteins and RNA. The 60kDa DNA/RNA binding protein and 52kDa T-cell regulatory protein are the best ... The antigen of anti-dsDNA antibodies is double stranded DNA.[37][38] ... Homogeneous immunofluorescence staining pattern of double stranded DNA antibodies on HEp-20-10 cells. Interphase cells show ...
DNA or RNA may be tethered in either single-stranded or double-stranded form, or entire structural motifs can be tethered, such ... A double-stranded DNA molecule is fixed with multiple binding sites on one end to a glass surface and on the other to a ... This can be interpreted as the separation of the two strands which corresponds to the denaturation of the molecule. In the high ...
"Single-stranded adenine-rich DNA and RNA retain structural characteristics of their respective double-stranded conformations ... Double Helix 1953-2003 National Centre for Biotechnology Education. *Genetic Education Modules for Teachers-DNA from the ... "Quiet debut for the double helix". Nature 421 (6921): 402-5. January 2003. doi:10.1038/nature01397. பப்மெட் 12540907. Bibcode: ... Basu H, Feuerstein B, Zarling D, Shafer R, Marton L (1988). "Recognition of Z-RNA and Z-DNA determinants by polyamines in ...
... (blue) producing mRNA (light-blue) from a double-stranded DNA template (orange). ... T7 RNA Polymerase is an RNA polymerase from the T7 bacteriophage that catalyzes the formation of RNA from DNA in the 5'→ 3' ... The T7 polymerase also requires a double stranded DNA template and Mg2+ ion as cofactor for the synthesis of RNA. It has a very ... RNA can be selectively synthesized from either strand of the insert DNA with the different polymerases. The enzyme is ...
Hepadnaviruses have very small genomes of partially double-stranded, partially single stranded circular DNA. The genome ... Inside this capsid the genome is converted from RNA to pdsDNA through activity of the polymerase as an RNA-dependent-DNA- ... a longer negative-sense strand and a shorter and positive-sense strand of variable length. In the virion these strands are ... This is then translocated to the nucleus, where the partially double stranded DNA is 'repaired' by the viral polymerase to form ...
The methylation of histone lysine has an important role in choosing the pathway for repairing DNA double-strand breaks.[21] As ... RNA polymerase control by chromatin structure. *Histone methylation. ReferencesEdit. *^ a b c d Wood A (2004). " ... Often, the β-strands found in the pre-SET domain will form β-sheets with the β-strands of the SET domain, leading to slight ... "The Dot1 histone methyltransferase and the Rad9 checkpoint adaptor contribute to cohesin-dependent double-strand break repair ...
Single-Strand Binding (SSB) Proteins. Bind to ssDNA and prevent the DNA double helix from re-annealing after DNA helicase ... Provides a starting point of RNA (or DNA) for DNA polymerase to begin synthesis of the new DNA strand. ... Re-anneals the semi-conservative strands and joins Okazaki Fragments of the lagging strand. ...
... Version 05 February 2006 (temporary). http://tolweb.org/Double-stranded_RNA_Viruses/21833/2006.02. ... Double-stranded RNA Viruses Click on an image to view larger version & data in a new window ... Transmission electron micrograph of intact rotavirus particles, double-shelled. Distinctive rim of radiating capsomeres. ... Double-stranded RNA Viruses Page Content. *Title Illustrations. *About This Page. articles & notes. *Double-stranded RNA ...
The positive-strand RNA can also be replicated by the RdRp to create a new double-stranded viral genome. Double-stranded RNA ... The double-stranded genome is used to transcribe a positive-strand RNA by the viral RNA-dependent RNA polymerase (RdRp). The ... Double-stranded RNA viruses (dsRNA viruses) are a polyphyletic group of viruses that have double-stranded genomes made of ... Double-stranded RNA viruses evolved two separate times from positive-strand RNA viruses. In the Baltimore classification system ...
A conserved double-stranded RNA-binding domain. D St Johnston, N H Brown, J G Gall, and M Jantsch ... We have identified a double-stranded (ds)RNA-binding domain in each of two proteins: the product of the Drosophila gene staufen ...
Small nucleolar RNA interference induced by antisense or double-stranded RNA in trypanosomatids ... double-stranded RNA;. GFP,. green fluorescent protein;. PFR,. paraflagellar rod;. 5′ UTR,. 5′ untranslated region. ... Double-stranded RNA induces mRNA degradation in Trypanosoma brucei. Huân Ngô, Christian Tschudi, Keith Gull, and Elisabetta ... Double-stranded RNA induces mRNA degradation in Trypanosoma brucei Message Subject (Your Name) has sent you a message from PNAS ...
The RNA has a region with double-stranded structure. Inhibition is sequence-specific in that the nucleotide sequences of the ... The present invention is distinguished from prior art interference in gene expression by antisense or triple-strand methods. ... A process is provided of introducing an RNA into a living cell to inhibit gene expression of a target gene in that cell. The ... duplex region of the RNA and of a portion of the target gene are identical. ...
This serine/threonine-specific protein kinase is activated by double-stranded RNA by a mechanism involving autophosphorylation ... PKR--a protein kinase regulated by double-stranded RNA.. Clemens MJ1. ... The RNA-regulated protein kinase, (PKR) is an interferon-inducible enzyme of widespread occurrence in eukaryotic organisms. ...
Double stranded RNA (dsRNA) can effectively reduce house fly fertility, and shows promise as a pest control method, according ... Double stranded RNA treatment can reduce fertility of adult house fly pests Fly-specific dsRNA interfered with gene expression ... Double Stranded RNA treatment Can Reduce Fertility of Adult House Fly Pests (IMAGE) view more ... Double stranded RNA (dsRNA) can effectively reduce house fly fertility, and shows promise as a pest control method, according ...
Double-stranded RNA is a trigger for apoptosis in vaccinia virus-infected cells.. Kibler KV1, Shors T, Perkins KB, Zeman CC, ... The vaccinia virus E3L gene codes for double-stranded RNA (dsRNA) binding proteins which can prevent activation of the dsRNA- ...
RNA interference (RNAi) is widely used as a reverse genetic approach for functional analysis of plant genes. Constitutive or ... 1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811.PubMed ... Double-stranded (ds) RNA interference (RNAi) is widely used as a reverse genetic approach for functional analysis of plant ... Jung H., Zhai Z., Vatamaniuk O.K. (2011) Direct Transfer of Synthetic Double-Stranded RNA into Protoplasts of Arabidopsis ...
The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nat. Immunol. 5: ... Microglia Recognize Double-Stranded RNA via TLR3. Terrence Town, David Jeng, Lena Alexopoulou, Jun Tan and Richard A. Flavell ... Microglia Recognize Double-Stranded RNA via TLR3 Message Subject (Your Name) has forwarded a page to you from The Journal of ... Recognition of double-stranded RNA and activation of NF-κB by Toll-like receptor 3. Nature 413: 732-738. ...
siRNA is a type of double stranded RNA (dsRNA).. The author stirred fears down under last year with well-publicized warnings ... RNA engineered to maintain toxic traits could also enter the natural environment to harm plants and animals, Heinemann argued. ... The papers authors, led by John Heinemann, warn that small interfering RNA (siRNA) used to silence genes could disrupt human ... Instead of adding genetic material for desirable traits, certain undesirable traits are "silenced" by inhibiting RNA from ...
... to result from a simple antisense mechanism that depends on hybridization between the injected RNA and endogenous messenger RNA ... Experimental introduction of RNA into cells can be used in certain biological systems to interfere with the function of an ... we found that double-stranded RNA was substantially more effective at producing interference than was either strand ... Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans Nature. 1998 Feb 19;391(6669):806-11. ...
RIG-I and MDA5 are cytosolic RNA sensors that play a critical role in innate antiviral responses. Major advances have been made ... IFN-α/β production does not rely on plus-strand RNA synthesis and thus generation of the partially double-stranded replicative ... Our results show that the incoming genomic plus-strand RNA does not activate MDA5, but minus-strand RNA synthesis and ... MDA5 detects the double-stranded RNA replicative form in picornavirus-infected cells Cell Rep. 2012 Nov 29;2(5):1187-96. doi: ...
Exerts its antiviral activity on a wide range of DNA and RNA viruses including hepatitis C virus (HCV), hepatitis B virus (HBV ... Microbial infection) Interacts with human herpes simplex virus 1 (HHV-1) protein US11 in an RNA-dependent manner (PubMed: ...
... edits RNA-binding protein Rnp4F. A-to-I editing of pre-mRNAs acts predominantly through nervous system targets to affect adult ... Has A-to-I RNA editing activity on extended dsRNA: ... Double-stranded RNA-specific editase AdarAdd BLAST. 676. ... Cluster: Double-stranded RNA-specific editase Adar. 4. Q9NII1-2. M9NGI0. Q9NII1-6. M9NFQ6. Drosophila melanogaster (Fruit fly) ... Cluster: Double-stranded RNA-specific editase Adar. 55. Q9NII1-2. M9NGI0. Q9NII1-6. M9NFQ6. UPI00078ADFB4. A0A0Q5T786. ...
... double stranded RNA (dsRNA)-activated serine/threonine kinase, PKR, is a potent negative regulator of cell growth when ... RNA, Double-Stranded / metabolism. Reverse Transcriptase Polymerase Chain Reaction. Tumor Cells, Cultured. eIF-2 Kinase / ... 0/Cell Cycle Proteins; 0/DNA Primers; 0/NF-kappa B; 0/RNA, Double-Stranded; EC 2.7.11.1/eIF-2 Kinase ... The interferon (IFN)-induced, double stranded RNA (dsRNA)-activated serine/threonine kinase, PKR, is a potent negative ...
Exerts its antiviral activity on a wide range of DNA and RNA viruses including west nile virus (WNV), sindbis virus (SV), foot- ... double-stranded RNA binding Source: MGI ,p>Inferred from Direct Assay,/p> ,p>Used to indicate a direct assay for the function, ... Interferon-induced, double-stranded RNA-activated protein kinaseAdd BLAST. 514. Amino acid modifications. Feature key. Position ... "Double-stranded RNA deaminase ADAR1 increases host susceptibility to virus infection.". Nie Y., Hammond G.L., Yang J.H.. J. ...
Double-stranded RNAs (dsRNAs) are widespread in plant pathogenic fungi, but their functions in fungal hosts remain mostly ... Double-stranded RNAs (dsRNAs) are widespread in plant pathogenic fungi, but their functions in fungal hosts remain mostly ... Sequencing of several cDNA clones derived from 6.0-kbp dsRNA revealed the presence of a RNA-dependent RNA polymerase (RDRP) ...
Double-stranded RNA (dsRNA) has been extracted from tissue of European mountain ash trees ( Sorbus aucupariaL.) showing typical ... Double-stranded RNA (dsRNA) has been extracted from tissue of European mountain ash trees (Sorbus aucuparia L.) showing typical ... Double-stranded RNA pattern and partial sequence data indicate plant virus infection associated with the ringspot disease of ... particularly to the RNA-dependent RNA polymerase of members of the family Bunyaviridae, but without high similarity to a known ...
Double-stranded and single-stranded RNA viruses of Saccharomyces cerevisiae. Annu. Rev. Microbiol.46:347-375. ... Evidence for common ancestry of a chestnut blight hypovirulence-associated double-stranded RNA and a group of positive-strand ... The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J. Gen. Virol.72:2197-2206. ... Double-Stranded RNA Mycovirus from Fusarium graminearum. Yeon-Mee Chu, Jae-Jin Jeon, Sang-Jin Yea, Yong-Ho Kim, Sung-Hwan Yun, ...
... and the regulatory domain prevents signaling in the absence of viral RNA. 5′-triphosphate and double-stranded RNA (dsRNA) are ... A host protein that recognizes invading viruses activates innate immunity defenses only when it senses both double-stranded RNA ... A host protein that recognizes invading viruses activates innate immunity defenses only when it senses both double-stranded RNA ... Cytosolic Viral Sensor RIG-I Is a 5-Triphosphate-Dependent Translocase on Double-Stranded RNA ...
Double-Stranded RNA and TGF-α Promote MUC5AC Induction in Respiratory Cells. Hiromi Tadaki, Hirokazu Arakawa, Takahisa Mizuno, ... Recognition of double-stranded RNA and activation of NF-κB by Toll-like receptor 3. Nature 413: 732-738. ... Synthetic double-stranded RNA induces multiple genes related to inflammation through Toll-like receptor 3 depending on NF-κB ... Double-stranded RNA activates RANTES gene transcription through co-operation of nuclear factor-κB and interferon regulatory ...
David Corey on Activation of gene expression by double-stranded RNA, part of a collection of online lectures. ... Activation of gene expression by double-stranded RNA. *Prof. David Corey - University of Texas Southwestern Medical Center, USA ... Corey, D. (2010, February 9). Activation of gene expression by double-stranded RNA [Video file]. In The Biomedical & Life ... Activation of gene expression by double-stranded RNA. Embed in course/own notes ...
Long-Cheng Li on Activation of gene expression by double-stranded RNAs, part of a collection of online lectures. ... The Ago protein would even discard one of the RNA strand in the RNA duplex. And it uses the remaining RNA strand as the guide ... The small RNA-Argonaute pathways and negative regulation of gene expression. *Targeting promoters by double-stranded RNA (dsRNA ... Activation of gene expression by double-stranded RNAs. *Prof. Long-Cheng Li - Peking Union Medical College Hospital, China ...
Structural Insight into the Mechanism of Double-Stranded RNA Processing by Ribonuclease III.. Gan, J., Tropea, J.E., Austin, B. ... Crystal structure of Aquifex aeolicus RNase III (D44N) complexed with product of double-stranded RNA processing. *DOI: 10.2210/ ... Members of the ribonuclease III (RNase III) family are double-stranded RNA (dsRNA) specific endoribonucleases characterized by ... Members of the ribonuclease III (RNase III) family are double-stranded RNA (dsRNA) specific endoribonucleases characterized by ...
URMC / Labs / Maquat Lab / Projects / Post-transcriptional Gene Regulation by Double-stranded RNA-binding Proteins ... We have found that STAU1, which is a double-stranded RNA binding protein, recruits the NMD factor UPF1 to certain mRNA 3- ... Post-transcriptional Gene Regulation by Double-stranded RNA-binding Proteins Project Collaborators:. Dr. Manuel Ares University ... Thus, STAU1 binding to 3UTR inverted Alu elements, like removal of these elements by alternative RNA 3-end cleavage and ...
Recognition of double-stranded RNA and activation of NF-kappaB by Toll-like receptor 3. Nature 2001;413:732-8. ... TLR3 as a Biomarker for the Therapeutic Efficacy of Double-stranded RNA in Breast Cancer. Bruno Salaun, Laurence Zitvogel, ... Here we show an example of this kind in which a drug [the double-stranded RNA (dsRNA) Poly (A:U)] can target its receptor TLR3 ... Adjuvant treatment with double-stranded RNA (dsRNA) was associated with a significant decrease in the risk of metastatic ...
1985 On the mechanism of exclusion of M2 double-stranded RNA by L-A-E double-stranded RNA in Saccharomyces cerevisiae. Yeast 1 ... 1989 The double-stranded RNA genome of yeast virus L-A encodes its own putative RNA polymerase by fusing two open reading ... We show that [KIL-d] does not reside on the double-stranded RNA genome of killer virus. Thus, the [KIL-d] effect on viral gene ... 1996 Double-stranded RNA viruses of Saccharomyces cerevisiae. Microbiol. Rev. 60: 250-265. ...
We reported previously that five genetically different double-stranded (ds... ... We reported previously that five genetically different double-stranded (ds) RNAs occur in these four isolates, with each ...
Since the discovery that short double-strand RNA molecules (siRNAs) can trigger sequence-specific degradation of target RNA in ... Piiper at the Saarland University discovered a way to defend double-stranded and partial double-stranded molecules of RNA - ... A new method that prevents the loss of silencing activity of double-strand RNA in humans. 03.08.2005 ...
  • Double-stranded RNA viruses (dsRNA viruses) are a polyphyletic group of viruses that have double-stranded genomes made of ribonucleic acid. (wikipedia.org)
  • Based on phylogenetic analysis of RdRp, the two clades do not share a common dsRNA ancestor but are instead separately descended from different positive-sense, single-stranded RNA viruses. (wikipedia.org)
  • The class Duplopiviricetes is the second clade of dsRNA viruses and is in the phylum Pisuviricota, which also contains positive-sense single-stranded RNA viruses. (wikipedia.org)
  • Double-stranded RNA (dsRNA) recently has been shown to give rise to genetic interference in Caenorhabditis elegans and also is likely to be the basis for phenotypic cosuppression in plants in certain instances. (pnas.org)
  • Transfection of synthetic α-tubulin 5′ UTR dsRNA, but not of either strand individually, caused the same phenotype. (pnas.org)
  • Double stranded RNA (dsRNA) can effectively reduce house fly fertility, and shows promise as a pest control method, according to a study published January 17, 2018 in the open-access journal PLOS ONE by Neil Sanscrainte from the USDA/ARS Center for Medical, Agricultural, and Veterinary Entomology, US, and colleagues. (eurekalert.org)
  • RNA interference using dsRNA has been suggested as an alternative control method. (eurekalert.org)
  • The authors of the present study designed dsRNA to target three fly RNA transcripts, the cytoskeletal protein actin-5C and two ribosomal proteins. (eurekalert.org)
  • Flies treated with M. domestica dsRNAs showed reduced levels of expression of the targeted transcripts, suggesting that the dsRNA was successfully targeting RNA transcripts before protein was produced. (eurekalert.org)
  • This study is the first to demonstrate that gene silencing using double stranded RNA (dsRNA) can be effective as a biopesticide for the adult housefly if improved delivery methods are subsequently developed," says Sanscrainte. (eurekalert.org)
  • The vaccinia virus E3L gene codes for double-stranded RNA (dsRNA) binding proteins which can prevent activation of the dsRNA-dependent, interferon-induced protein kinase PKR. (nih.gov)
  • siRNA is a type of double stranded RNA (dsRNA). (scientificamerican.com)
  • Has A-to-I RNA editing activity on extended dsRNA: edits RNA-binding protein Rnp4F. (uniprot.org)
  • The interferon (IFN)-induced, double stranded RNA (dsRNA)-activated serine/threonine kinase, PKR, is a potent negative regulator of cell growth when overexpressed in yeast or mammalian cells. (biomedsearch.com)
  • Sequencing of several cDNA clones derived from 6.0-kbp dsRNA revealed the presence of a RNA-dependent RNA polymerase (RDRP) gene. (apsnet.org)
  • Double-stranded RNA (dsRNA) has been extracted from tissue of European mountain ash trees ( Sorbus aucuparia L.) showing typical ringspot and mottling symptoms on leaves and a gradual decay in general. (springer.com)
  • Double-stranded RNA (dsRNA) viruses in some fungi are associated with hypovirulence and have been used or proposed as biological control agents. (asm.org)
  • Partial nucleotide sequences of the purified dsRNA identify an RNA-dependent RNA polymerase sequence and an ATP-dependent helicase that are closely related to those of Cryphonectria hypovirus and Barley yellow mosaic virus . (asm.org)
  • Double-stranded RNA (dsRNA) mycoviruses have been described for a wide variety of fungi and plant-pathogenic fungi ( 7 , 9 , 27 , 42 , 44 , 55 , 58 ). (asm.org)
  • These are RNA viruses that synthesize dsRNA during replication in infected cells. (jimmunol.org)
  • Members of the ribonuclease III (RNase III) family are double-stranded RNA (dsRNA) specific endoribonucleases characterized by a signature motif in their active centers and a two-base 3' overhang in their products. (rcsb.org)
  • A pattern of protein-RNA interactions, defined by four RNA binding motifs in RNase III and three protein-interacting boxes in dsRNA, is responsible for substrate specificity, while conserved amino acid residues and divalent cations are responsible for scissile-bond cleavage. (rcsb.org)
  • Adjuvant treatment with double-stranded RNA (dsRNA) was associated with a significant decrease in the risk of metastatic relapse in TLR3 positive but not in TLR3-negative breast cancers. (aacrjournals.org)
  • Here we show an example of this kind in which a drug [the double-stranded RNA (dsRNA) Poly (A:U)] can target its receptor TLR3 expressed on tumor cells leading to tumor regression in vivo . (aacrjournals.org)
  • The capsid and capsid-RNA polymerase proteins constitute the helper function that L-A dsRNA provides for M dsRNA satellite viral genomes. (genetics.org)
  • Production of double-stranded RNA (dsRNA) in a plant to affect the viability of a herbivorous animal is termed trans-kingdom RNAi (TK-RNAi). (unl.edu)
  • The double-stranded RNA (dsRNA)-dependent protein kinase (PKR) is a ubiquitously expressed serine-threonine kinase that is dramatically induced by interferon-γ. (aspetjournals.org)
  • Infection of cells with adenovirus or transfection of cells with double-stranded RNA (dsRNA) activates transcription of the alpha/beta interferon-stimulated genes (ISGs). (asm.org)
  • Double-stranded RNA (dsRNA) produced during viral infection activates several cellular antiviral responses ( 31 , 36 , 42 , 47 ). (asm.org)
  • RNA interference (RNAi) is a technique widely used for gene silencing in organisms and cultured cells, and depends on sequence homology between double-stranded RNA (dsRNA) and target mRNA molecules. (nih.gov)
  • In Drosophila, therefore, dsRNA is expressed in target cells as hairpin RNA (Section 3) using the Gal4/UAS system (Figure 1). (nih.gov)
  • When treated with double-stranded RNA (dsRNA), ΔTPR6-expressing cells exhibited a significant increase in eukaryotic initiation factor 2α phosphorylation and NF-κB activation, indicating a functional PKR. (asm.org)
  • The Klus phenotype is conferred by a medium-size double-stranded RNA (dsRNA) virus, Saccharomyces cerevisiae virus Mlus (ScV-Mlus), whose genome size ranged from 2.1 to 2.3 kb. (asm.org)
  • Mammalian melanoma differentiation-associated gene-5 (MDA5) and retinoic acid-inducible gene-I (RIG-I) selectively sense double-stranded RNA (dsRNA) according to length, as well as various RNA viruses to induce an antiviral response. (figshare.com)
  • Adenosine deaminase acting on dsRNA (ADAR1) isoforms neutralize the immunostimulatory activity of double-stranded RNA (dsRNA) by converting adenosine to inosine (i.e. (elifesciences.org)
  • ADAR1 alters the RNA coding sequence, because I is read as G, and it also destabilizes dsRNA because A:U base pairs are disrupted than I:U mismatches. (elifesciences.org)
  • Proviral effects are due in part to editing of viral RNAs ( Wong and Lazinski, 2002 ) and/or to destabilizing dsRNA resulting in suppression of dsRNA-signaling through MDA5 and MAVS to type I IFN genes ( Figure 1 ). (elifesciences.org)
  • OAS isoforms (OAS1, OAS2, OAS3) are IFN inducible enzymes that sense dsRNA and produce 2',5'-oligoadenylates (2-5A) which activate RNase L to degrade viral and host single-stranded RNAs leading to apoptosis and inhibition of virus growth ( Silverman and Weiss, 2014 ). (elifesciences.org)
  • We have identified that polyinosinic-polycytidylic Acid (poly I:C), a synthetic double-stranded RNA (dsRNA) molecule designed to mimic RNA virus infection, strongly induced the production of thymic stromal lymphopoietin (TSLP), a novel pro-allergic cytokine, in human corneal epithelium. (arvojournals.org)
  • Northern blot analysis revealed three dsRNAs in preparations of both dsRNA and total RNA from R . multiflora plants. (deepdyve.com)
  • Considering the important role for PKR in host defense against viruses, the independent duplication and fixation of PKR genes in different lineages probably provided selective advantages by leading to the recognition of an extended spectrum of viral nucleic acid structures, including both dsRNA and Z-DNA/RNA, and perhaps by altering sensitivity to viral PKR inhibitors. (biomedcentral.com)
  • Based on putative amino acid sequences, NS1 proteins are categorized into two gene pools, allele A and allele B. Here we identified that allele A NS1 proteins of H6N8 and H4N6 are able to inhibit double-stranded RNA (dsRNA)-induced activating protein-1 (AP-1) promoter in cultured cell lines (human A549 and mink lung cells). (lancs.ac.uk)
  • The core RNAi machinery is relatively well understood, however many of the systemic mechanisms, particularly double-stranded RNA (dsRNA) transport, are not. (edu.au)
  • Because of these properties, the initial stage in the search for fungi infected with mycoviruses is the detection of their viral genome, which in most of the described cases corresponds to double-stranded RNA (dsRNA). (biomedcentral.com)
  • However, Alternaria significantly inhibited production of IP-10, I-TAC and IFN-β, induced by viral double-stranded RNA (dsRNA) mimic poly I:C. TLR3 mRNA expression and protein production by poly I:C were significantly inhibited by Alternaria. (elsevier.com)
  • For example, a Dicer enzyme, which contains one dsRBD, binds to and slices dsRNA into 21-22 nucleotide long pieces that silence mRNA, and transactivation response RNA binding protein (TRBP) binds dsRNA and helps to position dsRNA in proper conformation for its cuting by Dicer. (uiuc.edu)
  • Interestingly, TRBP does not bind to duplex types other than dsRNA, namely dsDNA and DNA-RNA hybrids. (uiuc.edu)
  • Many other dsRBD proteins specifically bind to dsRNA duplexes, whereas some also weakly bind to DNA-RNA hybrid duplexes. (uiuc.edu)
  • Considering the experimental data about dsRBD binding targets, there are two questions of particular interest: (1) How do dsRBDs discriminate between nucleic acid duplexes of similar structures, such as dsRNA, DNA-RNA, and dsDNA? (uiuc.edu)
  • dsRNA minor grooves are lined with 2'-hydroxyl groups on sugar rings of RNA nucleotides, and the major grooves are lined with the negatively charged phosphate groups. (uiuc.edu)
  • Binding of TRBP-RBD2 to dsRNA (a), DNA-RNA (b), and dsDNA (c). (d) Contact areas between TRBP-RBD2 and the three duplexes. (uiuc.edu)
  • DNA-RNA and dsDNA duplexes stay in contact with a smaller number of TRBP-RBD2 residues than does dsRNA. (uiuc.edu)
  • Despite extensive research during the past decade elucidating the mechanism of RNA interference (RNAi) in insects, it is not clear how ingested or injected double-stranded RNA (dsRNA) triggers RNAi response in the whole body or even its progeny, which is referred to as systemic RNAi. (potatobeetle.org)
  • RNA present in the purified exosomes was analyzed to check if long dsRNA or siRNA is accumulated in them. (potatobeetle.org)
  • The ADAR gene specifically deaminates adenosine to inosine in double stranded (dsRNA). (moldiag.com)
  • These are called dsRNA where the RNA has two complementary strands, similar to the DNA found in all cells. (news-medical.net)
  • dsRNA forms the genetic material of some viruses (double-stranded RNA viruses). (news-medical.net)
  • double-stranded dna viruses is another non-enveloped, single-stranded rna virus, for example, an outbreak of hepatitis a associated with the consumption for example, viral double-stranded rna (dsrna) made during infection can be detected by the innate immune system, you can bet that so do viruses. (jeffho.com)
  • For example, viral double-stranded rna (dsrna) made during infection can be detected by the innate immune system, you can bet that so do viruses. (jeffho.com)
  • Staufen is a member of the family of double-stranded RNA (dsRNA)-binding proteins involved in the transport and/or localization of mRNAs to different subcellular compartments and/or organelles. (nih.gov)
  • These proteins are characterized by the presence of multiple dsRNA-binding domains which are required to bind RNAs having double-stranded secondary structures. (nih.gov)
  • Double-stranded RNA (dsRNA)-dependent protein kinase (PKR) is an interferon-induced protein kinase that plays a central role in the anti-viral process. (uky.edu)
  • Viral double-stranded RNA (dsRNA) is a ubiquitous intracellular "alert signal" used by cells to detect viral infection and to mount anti-viral responses. (elsevier.com)
  • For the detection of viral double-stranded RNA (dsRNA), sequence-dependent and -independent methods are available, such as quantitative real-time PCR and immunofluorescence, dot blot, ELISA or sequencing. (bio-protocol.org)
  • By atomic absorption analysis, we determined that the reovirus outer capsid protein sigma 3, which binds double-stranded RNA (dsRNA), is a zinc metalloprotein. (scienceexchange.com)
  • Sequence and structural requirements of RNA substrates were explored using various short dsRNA constructs. (ntu.edu.sg)
  • In addition, blunt-ended dsRNA as short as 10bp displayed good binding affinity to ADAR1 and ADARB1, suggesting the usefulness of short dsRNA substrates in protein-RNA co-crystallization. (ntu.edu.sg)
  • The recently identified phenomenon of double-stranded RNA (dsRNA)-mediated gene activation (RNAa) has been studied extensively, as it is present in humans, mice, and Caenorhabditis elegans , suggesting that dsRNA-mediated RNAa is an evolutionarily conserved mechanism. (biomedcentral.com)
  • Double-stranded RNA (dsRNA) has been applied to control insect pests by its suppressive activity against specific target genes. (koreascience.or.kr)
  • They are descended from a common ancestor that was a double-stranded RNA (dsRNA) virus, and they are considered to be a sister clade of reoviruses, which are dsRNA viruses. (wikipedia.org)
  • We have identified a double-stranded (ds)RNA-binding domain in each of two proteins: the product of the Drosophila gene staufen, which is required for the localization of maternal mRNAs, and a protein of unknown function, Xlrbpa, from Xenopus. (pnas.org)
  • PKR--a protein kinase regulated by double-stranded RNA. (nih.gov)
  • The RNA-regulated protein kinase, (PKR) is an interferon-inducible enzyme of widespread occurrence in eukaryotic organisms. (nih.gov)
  • This serine/threonine-specific protein kinase is activated by double-stranded RNA by a mechanism involving autophosphorylation. (nih.gov)
  • Microbial infection) Interacts with human herpes simplex virus 1 (HHV-1) protein US11 in an RNA-dependent manner (PubMed:11836380). (rcsb.org)
  • Cell cycle regulation of the double stranded RNA activated protein kinase, PKR. (biomedsearch.com)
  • Retinoic acid inducible-gene I (RIG-I) is a cytosolic multidomain protein that detects viral RNA and elicits an antiviral immune response. (sciencemag.org)
  • The Ago protein would even discard one of the RNA strand in the RNA duplex. (hstalks.com)
  • The nuclear function of small RNAs and the protein partners Argonautes is naturally alone, except in plants and in some lower eukaryotes, such as fission yeast and Drosophila. (hstalks.com)
  • A 7 residue linker within the protein facilitates induced fit in protein-RNA recognition. (rcsb.org)
  • We have found that STAU1, which is a double-stranded RNA binding protein, recruits the NMD factor UPF1 to certain mRNA 3'-untranslated regions (3'UTRs) so as to elicit SMD in a translation-dependent mechanism (reviewed in Park and Maquat, 2013, Wiley Interdiscip Rev RNA 4:423-435). (rochester.edu)
  • Asymmetric segregation of the double-stranded RNA binding protein Staufen2 during mammalian neural stem cell divisions promotes lineage progression. (biomedsearch.com)
  • Here, we show that the double-stranded RNA-binding protein Stau2 is distributed asymmetrically during progenitor divisions in the developing mouse cortex, preferentially segregating into the Tbr2(+) neuroblast daughter, taking with it a subset of RNAs. (biomedsearch.com)
  • The interferon-induced, double-stranded RNA-dependent protein kinase (PKR) can play critical roles in inhibiting virus replication and inducing apoptosis. (aspetjournals.org)
  • Possible involvement of double-stranded RNA-activated protein kinase in cell death by influenza virus infection. (asm.org)
  • Double-stranded (ds) RNA, generated during viral infection, binds and activates the mammalian anti-viral protein kinase PKR, which phosphorylates the translation initiation factor eIF2α leading to the general inhibition of protein synthesis. (biomedcentral.com)
  • Chimeric forms of NS1 protein, composed of either RNA binding domain of allele A or B and effector domain of allele A or B, showed comparable inhibition to that of their wild-type NS1 proteins, or to the effector domain of corresponding NS1 proteins. (lancs.ac.uk)
  • The 353 bp Cx 43 double-stranded RNA was microinjected into in vitro fertilized ovine zygotes, and the levels of target mRNA and protein were investigated. (koreascience.or.kr)
  • 1989. Abnormal development and dye coupling produced by antisense RNA to gap junction protein in mouse preimplantation embryos. (koreascience.or.kr)
  • Prevention of the β-amyloid peptide-induced inflammatory process by inhibition of double-stranded RNA-dependent protein kinase in primary murine mixed co-cultures. (inserm.fr)
  • In virus-infected cells, double-stranded RNA-dependent protein kinase (PKR) controls the NF-κB signaling pathway. (inserm.fr)
  • DSB repair by transcript RNA in cis is promoted by the HR protein Rad52 but not Rad51, in agreement with the demonstration that the yeast and human Rad52 proteins efficiently catalyze annealing of RNA to a DSB-like DNA end in vitro. (gatech.edu)
  • The interferon-induced, double-stranded RNA-activated protein kinase (PKR) has been implicated in processes that rely on apoptosis as control mechanisms in vivo, including antiviral activities, cell growth regulation, and tumorigenesis. (monash.edu)
  • The P68 protein (referred to as P68 on the basis of its molecular weight of 68,000 in human cells) is a serine/threonine kinase induced by interferon treatment and activated by double-stranded (ds) RNAs. (pasteur.fr)
  • Interestingly, both the mutant and wild-type protein kinases efficiently bound activator dsRNAs despite the fact that only the latter was activated by these RNAs. (pasteur.fr)
  • protein synthesis can be blocked by interfering RNA. (uiuc.edu)
  • For example, genes in their RNA forms serve as templates for synthesis of new proteins, whereas non-coding RNA can bind the copied genes and silence protein synthesis. (uiuc.edu)
  • Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). (pasteur.fr)
  • Double-stranded RNA-binding protein 4 (DRB4) plays a role in RNA-mediated post-transcriptional gene silencing (PTGS). (agrisera.com)
  • Stress granules regulate double-stranded RNA-dependent protein kinase activation through a complex containing G3BP1 and Caprin1. (viictr.org)
  • For example, the messenger RNA (mRNA) carries the information from the DNA to the ribosome in the cytoplasm where the actual protein synthesis (translation) takes place. (news-medical.net)
  • The mRNA carries the genetic code from the DNA into the cytoplasm to the ribosomes for translation of the RNA into a protein or polypeptide strand. (news-medical.net)
  • Whereas the roles of protein-DNA interactions in HR and NHEJ have been fairly well defined, the functions of small and long non-coding RNAs and RNA-DNA hybrids in the DNA damage response is just beginning to be elucidated. (preprints.org)
  • However, mass spectroscopy identified a 50-kDa band (six peptide sequences that migrated slightly above the contaminating MEP50 band) corresponding to the human immunodeficiency virus (HIV)-1 transactivating response (TAR) RNA-binding protein (TRBP) 10 . (nature.com)
  • The TRBP gene encodes a protein with three double-stranded RNA-binding domains (dsRBDs). (nature.com)
  • Double-Stranded RNA-Dependent Protein Kinase Regulates the Motility of" by Mei Xu, Gang Chen et al. (uky.edu)
  • Ribosomes are complexes of RNA and protein that are found in all cells. (gettyimages.com)
  • Distinct binding sites for zinc and double-stranded RNA in the reovirus outer capsid protein sigma 3. (scienceexchange.com)
  • RNA activated/dependent protein kinase (PKR) is a serine threonine kinase that can directly couple to the metabolic pathway due to its catalytic activity and has a role in pathogen recognition. (medcraveonline.com)
  • The results provide the basis to further study ADAR protein-RNA binding and catalysis. (ntu.edu.sg)
  • The positive-strand RNA may be used as messenger RNA (mRNA) which can be translated into viral proteins by the host cell's ribosomes. (wikipedia.org)
  • Instead of adding genetic material for desirable traits, certain undesirable traits are "silenced" by inhibiting RNA from carrying the genetic base pairs from the DNA to synthesize proteins. (scientificamerican.com)
  • Finally, a cDNA fragment of 3,737 bp was obtained, which showed homology to viral proteins, particularly to the RNA-dependent RNA polymerase of members of the family Bunyaviridae , but without high similarity to a known genus. (springer.com)
  • Fly strains expressing Gal4 proteins in a spatiotemporally regulated manner under the control of enhancers are genetically crossed with fly strains bearing a gene expressing hairpin RNA downstream of an UAS. (nih.gov)
  • CTV genome is composed of a single stranded, positive sense, RNA of 19296 nucleotides organized in 12 open reading frames which encodes at least 17 proteins (Karasev et al . (scialert.net)
  • 1999). The genomic RNA is encapsidadet by two proteins of 25 and 27 kDa, coating about 95 and 5% of the particle length, respectively (Febres et al . (scialert.net)
  • however, the precise role that P-bodies and their component proteins play in small interfering RNA (siRNA)-mediated RNAi remains unclear. (pubmedcentralcanada.ca)
  • LGP 2‐mediated antagonism of ds RNA ‐mediated RNA i may help ensure that viral ds RNA substrates are preserved in order to serve as targets of antiviral ISG proteins. (embopress.org)
  • Here we show that the CP of amalgaviruses is homologous to the nucleocapsid proteins of negative-strand RNA viruses of the genera Phlebovirus (Bunyaviridae) and Tenuivirus. (pasteur.fr)
  • Class IV ssRNA viruses have positive-sense RNA genomes, meaning they can be directly read by ribosomes to translate into proteins. (news-medical.net)
  • The RNA editing capacity of the proteins makes ADARs major players in the regulation of important gene products, modulation of immune responses, outcome of viral infections, oncogenesis, and even developmental processes. (ntu.edu.sg)
  • As new nucleotide sequences are synthesized by RdRp, capsid proteins are assembled and encapsidate the newly replicate viral RNA. (wikipedia.org)
  • Some -ssRNA viruses are ambisense, meaning that both the negative genomic strand and positive antigenome separately encode different proteins. (wikipedia.org)
  • The present invention is distinguished from prior art interference in gene expression by antisense or triple-strand methods. (google.com)
  • Double-stranded (ds) RNA interference (RNAi) is widely used as a reverse genetic approach for functional analysis of plant genes. (springer.com)
  • 1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans . (springer.com)
  • Zamore, P. D. (2001) RNA interference: listening to the sound of silence. (springer.com)
  • Zhai, Z., Sooksa-nguan, T., and Vatamaniuk, O. K. (2009) Establishing RNA interference as a reverse-genetic approach for gene functional analysis in protoplasts. (springer.com)
  • RNA interference has been used in the nematode Caenorhabditis elegans to manipulate gene expression. (nih.gov)
  • To our surprise, we found that double-stranded RNA was substantially more effective at producing interference than was either strand individually. (nih.gov)
  • After injection into adult animals, purified single strands had at most a modest effect, whereas double-stranded mixtures caused potent and specific interference. (nih.gov)
  • Only a few molecules of injected double-stranded RNA were required per affected cell, arguing against stochiometric interference with endogenous mRNA and suggesting that there could be a catalytic or amplification component in the interference process. (nih.gov)
  • RNA interference (RNAi) was discovered almost 20 years ago and has been exploited worldwide to silence genes in plants and animals. (unl.edu)
  • RNA interference (RNAi) is a powerful homology-based gene silencing mechanism directed by small RNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs). (pubmedcentralcanada.ca)
  • In contrast, the IFN system is absent in plants and invertebrates, which defend themselves from viral intruders using RNA interference ( RNA i). (embopress.org)
  • RNA interference ( RNA i) is inefficient as an antiviral mechanism in mammals in part because it is suppressed by the type I interferon ( IFN ) pathway. (embopress.org)
  • RNA interference (RNAi) has become a widely utilized method for studying gene function, yet despite this many of the mechanisms surrounding RNAi remain elusive. (edu.au)
  • RNA interference (RNAi) is an acknowledged useful and effective tool to study gene function in various cells. (koreascience.or.kr)
  • Double-stranded RNA in exosomes: Potential systemic RNA interference pathway in the Colorado potato beetle, Leptinotarsa decemlineata. (potatobeetle.org)
  • Shu YH, Wang JW, Lu K, Zhou JL, Zhou Q, Zhang GR. The first vitellogenin receptor from a Lepidopteran insect: molecular characterization, expression patterns and RNA interference analysis. (viictr.org)
  • 21-22 nt) for example are found in eukaryotes and act through RNA interference (RNAi). (news-medical.net)
  • Recent advances in RNA interference (RNAi) technology make it possible to manipulate mosquito gene function in vivo and to determine the effects of mosquito gene regulation on the ability to support the growth of Plasmodium. (genetics.org)
  • We silenced the expression of the transcript using RNA interference, and at 2 weeks after feeding, insects with reduced Rhopr-IGF expression showed increased hemolymph lipid and carbohydrate levels when compared to controls, but no differences were observed in fat body lipid or carbohydrate content. (frontiersin.org)
  • Integrin ${\beta}$ subunit and its RNA interference in immune and developmental processes of the Oriental tobacco budworm, Helicoverpa assulta. (koreascience.or.kr)
  • RNA interference of cadherin gene ex pression in Spodoptera exigua reveals its significance as a specific Bt target. (koreascience.or.kr)
  • RNA interference of ${\beta}$ 1 integrin subunit impairs development and immune responses of the beet armyworm, Spodoptera exigua. (koreascience.or.kr)
  • RNA interference in the light brown apple moth, Epiphyas postvittana (Walker) induced by double-stranded RNA feeding. (koreascience.or.kr)
  • The double-stranded genome is used to transcribe a positive-strand RNA by the viral RNA-dependent RNA polymerase (RdRp). (wikipedia.org)
  • Furthermore, in these organisms, RNA polymerase II promoters have not been identified. (pnas.org)
  • RNA was synthesized from linear DNA templates by using the Ampliscribe T7 RNA polymerase kit from Epicentre Technologies (Madison, WI). (pnas.org)
  • Sastry, S. S. and Ross, B. M. (1997) Nuclease activity of T7 RNA polymerase and the heterogeneity of transcription elongation complexes. (springer.com)
  • Three double-stranded RNA segments of bacteriophage phi 6 (L, M, and S) were transcribed in vitro by a virion-associated RNA polymerase. (semanticscholar.org)
  • Color enhanced platinum-shadowed electron micrograph (freeze-fracture TEM) showing characteristic attachment of RNA polymerase molecules to DNA strands. (gettyimages.com)
  • Class V viruses have a negative-sense RNA genome, meaning they must be transcribed by a viral polymerase to produce a readable strand of mRNA. (news-medical.net)
  • They have genomes that act as complementary strands from which messenger RNA (mRNA) is synthesized by the viral enzyme RNA-dependent RNA polymerase (RdRp). (wikipedia.org)
  • Their genomes are negative sense, meaning that messenger RNA (mRNA) can be synthesized directly from the genome by the viral enzyme RNA-dependent RNA polymerase (RdRp), also called RNA replicase, which is encoded by all -ssRNA viruses. (wikipedia.org)
  • So my topic on small-RNAs or sRNAs, such as siRNAs and the microRNAs are known to trigger an evolutionary conservative phenomenon, known as RNAi. (hstalks.com)
  • By placing genes expressing hairpin RNAs downstream of an UAS, RNAi is readily induced by genetic crossing. (nih.gov)
  • Double‐stranded RNA induces a post‐transcriptional gene silencing process, termed RNAi, in diverse organisms. (embopress.org)
  • Similar to the double‐stranded RNA involved in RNAi, this promoter double‐stranded RNA, which is synthesized in the nucleus, is partially cleaved into small RNAs ∼23 nucleotides in length. (embopress.org)
  • We have observed that challenging Trypanosoma brucei cells with gene-specific double-stranded RNAs (dsRNAs) leads to specific degradation of the homologous mRNA. (pnas.org)
  • Double-stranded RNAs (dsRNAs) are widespread in plant pathogenic fungi, but their functions in fungal hosts remain mostly unclear, with a few exceptions. (apsnet.org)
  • Double-stranded RNAs (dsRNAs) are a common by-product of viral replication and are potent activators of antiviral immunity via the production of type I interferon (IFN) and other pro-inflammatory cytokines (Nellimarla and Mossman, 2014). (bio-protocol.org)
  • Both diseases have similar symptoms three taxa typically infect fungi, and because microscopy and are associated with a complex pattern of double- observations have identified a fungus-like organism in the stranded RNAs (dsRNAs), absent from healthy-looking affected leaf tissues [6], these data support a fungal eti- material [1]. (deepdyve.com)
  • Here, we report that pretreatment of prostate cancer PC-3 cells with IFNs sensitized these cells to double-stranded RNAs (dsRNAs)-induced apoptosis. (csuohio.edu)
  • these types of dsRNAs are referred to as small activating RNAs (saRNAs). (biomedcentral.com)
  • Although much is known regarding the mechanisms of gene silencing by small dsRNAs in human cells, little is known about the mechanism of RNA-induced gene activation. (biomedcentral.com)
  • The positive-strand RNA can also be replicated by the RdRp to create a new double-stranded viral genome. (wikipedia.org)
  • We show that [KIL-d] does not reside on the double-stranded RNA genome of killer virus. (genetics.org)
  • Therefore, [KIL-d] appears to interact with the nucleus in order to exert its effects on gene expression by the killer virus RNA genome. (genetics.org)
  • This regulation appears to involve the nucleus of the host cell and is the first example that we are aware of in which an epigenetic phenomenon alters phenotypic expression of a viral RNA genome. (genetics.org)
  • A double-strand break (DSB) is one of the most deleterious DNA lesions and its repair is crucial for genome stability. (gatech.edu)
  • Our study provides proof and initial characterization of a new mechanism of DNA repair and HR mediated by RNA in yeast, and unravels novel aspects in the complex relationship between RNA and DNA in genome stability. (gatech.edu)
  • While genes comprise less than 2% of our DNA, up to 80% of the genome is copied into RNA molecules that can execute the instructions stored in DNA. (uiuc.edu)
  • We present a genome-wide approach to map DNA double-strand breaks (DSBs) at nucleotide resolution by a method we termed BLESS (direct in situ breaks labeling, enrichment on streptavidin and next-generation sequencing). (nature.com)
  • Group VI viruses have a positive sense, single-stranded RNA genome, but replicate through a DNA intermediate. (news-medical.net)
  • The RNA is converted to DNA by reverse transcriptase and then the DNA is spliced into the host genome for subsequent transcription and translation using the enzyme integrase. (news-medical.net)
  • Class VII viruses have a double-stranded DNA genome, but unlike Class I viruses, they replicate via a ssRNA intermediate. (news-medical.net)
  • To reproduce the genome, RNA is reverse transcribed back to DNA. (news-medical.net)
  • During replication of the viral genome, RdRp synthesizes a positive-sense antigenome that it uses as a template to create genomic negative-sense RNA. (wikipedia.org)
  • Negative-strand RNA viruses also share a number of other characteristics: most contain a viral envelope that surrounds the capsid, which encases the viral genome, -ssRNA virus genomes are usually linear, and it is common for their genome to be segmented. (wikipedia.org)
  • However, the nuclear function of this small RNA-Ago pathways in mammalian cells remains a mystery, which will be the topic of my presentation today. (hstalks.com)
  • The group of Dr. Dr. Albrecht Piiper at the Saarland University discovered a way to defend double-stranded and partial double-stranded molecules of RNA - particularly siRNAs - from degradation by RNAse in mammalian body fluid including humans. (innovations-report.com)
  • An Asymmetrically Localized Staufen2-Dependent RNA Complex Regulates Maintenance of Mammalian Neural. (biomedsearch.com)
  • Interestingly, the RNA i machinery is conserved in mammals, and we have recently demonstrated that it is able to participate in mammalian antiviral defence in conditions in which the IFN system is suppressed. (embopress.org)
  • Thus, the inefficiency of RNA i as a mechanism of antiviral defence in mammalian somatic cells can be in part attributed to Dicer inhibition by LGP 2 induced by type I IFN s. (embopress.org)
  • Double-stranded RNA is a trigger for apoptosis in vaccinia virus-infected cells. (nih.gov)
  • The papers' authors, led by John Heinemann, warn that small interfering RNA (siRNA) used to silence genes could disrupt human cells. (scientificamerican.com)
  • We show that upon transfection into cells, siRNAs rapidly localize to P-bodies in their native double-stranded conformation, as indicated by fluorescence resonance energy transfer imaging and that Ago2 is at least in part responsible for this siRNA localization pattern, indicating RISC involvement. (pubmedcentralcanada.ca)
  • In vitro reconstitution assays demonstrated that TRBP is required for the recruitment of Ago2 to the small interfering RNA (siRNA) bound by Dicer. (nature.com)
  • Heinemann, U. and Saenger, W. (1983) Crystallographic study of mechanism of ribonuclease T1-catalysed specific RNA hydrolysis. (springer.com)
  • Such effects have been proposed to result from a simple antisense mechanism that depends on hybridization between the injected RNA and endogenous messenger RNA transcripts. (nih.gov)
  • The structure reveals a wealth of information about the mechanism of RNA hydrolysis that can be extrapolated to other RNase III family members. (rcsb.org)
  • This result could be explained by a mechanism in which transcript RNA repairs a DSB in conditions of limited end resection via an inverse strand exchange reaction. (gatech.edu)
  • Repair of DNA double strand break (DSB) is an important mechanism for maintaining genetic stability during a DNA damage event. (frontiersin.org)
  • Understanding the mechanism behind ADARs' RNA substrate binding and catalysis would shed light on mechanisms of diseases related to ADAR dysfunction. (ntu.edu.sg)
  • In recent years, the regulation of gene expression by non-coding RNAs (ncRNAs) has become recognized as an evolutionarily conserved mechanism in biology. (biomedcentral.com)
  • 15. The method of claim 12 in which said double-stranded ribonucleic acid structure is at least 25 bases in length and each of the ribonucleic acid strands is able to specifically hybridize to a deoxyribonucleic acid strand of the target gene over the at least 25 bases. (google.com)
  • an rna virus is a virus that has rna (ribonucleic acid) as its genetic material. (jeffho.com)
  • Double-stranded rna species at single-cell level and identify key extreme example of convergent hela cell infection with the positive-strand rna virus an rna virus is a virus that has rna (ribonucleic acid) as its genetic material. (jeffho.com)
  • Negative-strand RNA viruses (-ssRNA viruses) are a group of related viruses that have negative-sense, single-stranded genomes made of ribonucleic acid. (wikipedia.org)
  • Smoking decreases the response of human lung macrophages to double-stranded RNA by reducing TLR3 expression. (viictr.org)
  • Small interfering RNA knockdown revealed that TLR3 mediated VSMC activation by poly(I:C), whereas melanoma differentiation-associated gene 5 was more important for VSMC stimulation by self-RNA. (elsevier.com)
  • Since the discovery that short double-strand RNA molecules (siRNAs) can trigger sequence-specific degradation of target RNA in cells, great efforts are going on throughout the world to use siRNAs in human therapy. (innovations-report.com)
  • In special cases, HR can occur between RNA molecules, such as RNA molecules in RNA viruses. (gatech.edu)
  • However, very little is known about RNA-DNA HR. Previously, it was demonstrated that synthetic RNA-containing molecules can serve as templates for repairing defective or broken homologous chromosomal DNA in yeast, human and bacterial cells, but it remained unclear whether cellular RNA transcripts can recombine with genomic DNA. (gatech.edu)
  • One of the first ribozymes to be discovered was RNase P, a ribonuclease that is involved in generating tRNA molecules from larger, precursor RNAs. (news-medical.net)
  • MicroRNAs (miRNAs) are generated by a two-step processing pathway to yield RNA molecules of approximately 22 nucleotides that negatively regulate target gene expression at the post-transcriptional level 1 . (nature.com)
  • Ribosomal RNA molecules from human cells. (gettyimages.com)
  • Binds double-stranded RNA (regardless of the sequence) and tubulin. (nih.gov)
  • 4 , 5 , 12 -14 In the presence of a pathogen, the double stranded RNA binds to the N-terminal of the PKR enzyme and leads to the phosphorylation of eukaryotic initiation factor (eIF2A). (medcraveonline.com)
  • Our results show that the incoming genomic plus-strand RNA does not activate MDA5, but minus-strand RNA synthesis and production of the 7.5 kbp replicative form trigger a strong IFN-α/β response. (nih.gov)
  • Positive clones were further analysed by using them as hybridisation probes in Northern blots of total plant RNA and in Southern hybridisation with genomic DNA from Sorbus aucuparia leaves. (springer.com)
  • 1995) and the changeable number of defective RNAs that contain both genomic RNA termini but lack variable portions of the central region (Mawassi et al . (scialert.net)
  • DNA double-strand breaks (DSBs) are deleterious lesions that are generated in response to ionizing radiation or replication fork collapse that can lead to genomic instability and cancer. (preprints.org)
  • 2007, EMBO J, 26:2670-2681) but also by intermolecular base-pairing either between the Alu element of an mRNA 3'UTR and a partially complementary Alu element in one or more Alu element-containing long noncoding (lnc)RNAs (Gong and Maquat, 2011, Nature, 470:284-288) or between the 3'UTR Alu elements of two different mRNAs (Gong et al. (rochester.edu)
  • In RNA i, the endoribonuclease Dicer cleaves virus‐derived double‐stranded RNA (ds RNA ) into small interfering RNA s (si RNA s) that target complementary viral RNA for cleavage. (embopress.org)
  • each side can be used as a pattern to replicate its' complementary strand. (coursehero.com)
  • each separated strand is used as a template for synthesis of a new complementary strand. (coursehero.com)
  • Synthesis will proceed in opposite directions along the complementary strands of DNA. (coursehero.com)
  • This results in two identical strands of DNA-each with one "original" string of sugars and Nucleotide bases and one complementary "daughter" strand, cross-linked by the complementary nucleotides. (coursehero.com)
  • the other strand is synthesized in small fragments , which are then bonded together by DNA ligase enzymes to build the complementary strand. (coursehero.com)
  • 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. (viictr.org)
  • It assists DCL4 during biogenesis of trans-acting small interferring RNAs (ta-siRNAs) and is necessary for DCL4 activity. (agrisera.com)
  • 20-25 nt) are often produced by breakdown of viral RNA, there are also endogenous sources of siRNAs. (news-medical.net)
  • Over the last 10 years, the study of RNA metabolism in trypanosomatid protozoa has unraveled novel mechanisms of eukaryotic gene expression such as polycistronic transcription ( 1 ), trans-splicing ( 2 , 3 ), mitochondrial RNA editing ( 4 - 6 ), and coupling of trans-splicing and polyadenylation ( 7 ). (pnas.org)
  • A process is provided of introducing an RNA into a living cell to inhibit gene expression of a target gene in that cell. (google.com)
  • 2000) Gene expression: total silencing by intron-spliced hairpin RNAs. (springer.com)
  • Further, we show that in differentiated cells lacking components of the IFN response, ectopic expression of LGP 2 interferes with RNA i‐dependent suppression of gene expression. (embopress.org)
  • These RNAs serve to regulate the process of gene expression. (news-medical.net)
  • MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA). (osti.gov)
  • Because the DNA methylation changes seen in both types of silencing are confined largely to regions of sequence homology between interacting genes, sequence‐specific methylation signals consisting of either DNA-DNA or RNA-DNA associations are believed to be involved. (embopress.org)
  • These are encoded by RNA genes and also derived from mRNA introns. (news-medical.net)
  • Inhibition is sequence-specific in that the nucleotide sequences of the duplex region of the RNA and of a portion of the target gene are identical. (google.com)
  • LGP 2 inhibition of Dicer may have evolved to preserve ds RNA for stimulation of interferon‐dependent immunity. (embopress.org)
  • RIG-I and MDA5 are cytosolic RNA sensors that play a critical role in innate antiviral responses. (nih.gov)
  • Exerts its antiviral activity on a wide range of DNA and RNA viruses including hepatitis C virus (HCV), hepatitis B virus (HBV), measles virus (MV) and herpes simplex virus 1 (HHV-1). (rcsb.org)
  • Exerts its antiviral activity on a wide range of DNA and RNA viruses including west nile virus (WNV), sindbis virus (SV), foot-and-mouth virus (FMDV), semliki Forest virus (SFV) and lymphocytic choriomeningitis virus (LCMV). (uniprot.org)
  • Since exposure to rhinovirus or double-stranded (ds) RNA (a surrogate of viral infection) induces TSLP expression in bronchial epithelial cells (BECs), this cytokine may link innate antiviral responses and the type 2 adaptive immune response. (bmj.com)
  • In response to viral infection, cells activate a variety of antiviral responses, including several that are triggered by double-stranded (ds) RNA. (asm.org)
  • Interferon antagonism was strictly dependent on RNA binding, and chimeric bat influenza viruses expressing NS1s defective in this activity were highly attenuated in interferon-competent cells but not in cells unable to establish antiviral immunity. (uzh.ch)
  • The antiviral effects are due to hyper-editing and mutagenesis of viral RNAs ( Samuel, 2011 ). (elifesciences.org)
  • In contrast, when the IFN system is active, one or more ISG s act to mask or suppress antiviral RNA i. (embopress.org)
  • Here, we demonstrate that LGP 2 constitutes one of the ISG s that can inhibit antiviral RNA i in mammals. (embopress.org)
  • The antiviral effect of vp28 or vp26 double-stranded (ds) RNA upon single or consecutive white spot syndrome virus (WSSV) intramuscular challenges with a high infectious dose was evaluated. (semanticscholar.org)
  • Induction of antiviral immunity by double-stranded RNA in a marine invertebrate. (semanticscholar.org)
  • Double-helical DNA is capable of forming triple-helical structures through Hoogsteen and reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidence that microRNAs form triple-helical structures with duplex DNA, and identify microRNA sequences that favor triplex formation. (osti.gov)
  • We show that LGP 2 associates with Dicer and inhibits cleavage of ds RNA into si RNA s both in vitro and in cells. (embopress.org)
  • LGP 2 inhibits Dicer‐dependent processing of ds RNA , a prerequisite for RNA i. (embopress.org)
  • Double-stranded RNA pattern and partial sequence data indicate plant virus infection associated with the ringspot disease of European mountain ash ( Sorbus aucuparia L. (springer.com)
  • Thus, there is great potential in developing chemical probes and therapeutic ligands for the recognition of RNA sequence and structure. (jove.com)
  • Chemically modified Peptide Nucleic Acid (PNA) oligomers have been recently developed that can recognize RNA duplexes in a sequence-specific manner. (jove.com)
  • The technique presented here is sequence-independent and is well detailed in the following protocol, taking the example of Leishmania RNA virus (LRV) in Leishmania guyanensis ( Lgy ) species. (bio-protocol.org)
  • The technique presented here is sequence-independent, in comparison to quantitative real-time PCR, so it can be applied widely to RNA viruses. (bio-protocol.org)
  • At the leader sequence, RdRp synthesizes a 5-'end (usually pronounced "five prime end") triphosphate-leader RNA and either, in the case of the subphylum Haploviricotina, caps the 5'-end or, in the case of the subphylum Polyploviricotina, snatches a cap from a host mRNA and attaches it to the viral mRNA so that the mRNA can be translated by the host cell's ribosomes. (wikipedia.org)
  • CPV exhibits striking capsid stability and is fully capable of endogenous RNA transcription and processing. (wikipedia.org)
  • Experimental introduction of RNA into cells can be used in certain biological systems to interfere with the function of an endogenous gene. (nih.gov)
  • These findings suggest that IFN-γ, and by inference adaptive immunity, sensitizes the vasculature to innate immune activators, such as RNA, and activation of IFN-γ-primed vascular cells by exogenous or endogenous sources of RNA may contribute to the inflammatory milieu of arteriosclerosis. (elsevier.com)
  • If the guide RNA is a microRNA, they often bind to the 3'UTR region of mRNA, resulting in mRNA degradation and/or suppression of the translation. (hstalks.com)
  • Both transcriptional and post‐transcriptional gene silencing can thus be initiated by double‐stranded RNAs that enter the same degradation pathway. (embopress.org)
  • This step destabilizes the RNA helix and renders it susceptible to further modification such as editing and degradation, so this process play a role in post-transcriptional RNA editing and RNA virus infections. (moldiag.com)
  • Double-stranded RNA is a potent pathogen-associated molecular pattern (PAMP) produced as a by-product of viral replication and a well-known hallmark of viral infection. (bio-protocol.org)
  • Double-stranded RNA viruses evolved two separate times from positive-strand RNA viruses. (wikipedia.org)
  • medicinenet examples of positive-strand rna viruses include polio virus, coxsackie virus, and echovirus. (jeffho.com)
  • In plants, the small RNA-Ago pathway can initiate lower DNA methylation, a phenomenon known as RNA-directed DNA methylation or RdDM, leading to transcriptional gene silencing. (hstalks.com)
  • In fission yeast and in Drosophila, RNA pathway can mediate the assembly and maintenance of heterochromatin at the centromere regions, which is required to silence repetitive sequences. (hstalks.com)
  • Notwithstanding our present limited knowledge of these subjects, it appears that trypanosome mRNA abundance is primarily, if not solely, regulated at the level of RNA metabolism rather that at the level of transcription initiation, as is the case in most eukaryotic organisms. (pnas.org)
  • Mlus positive strands carry cis -acting signals at their 5′ and 3′ termini for transcription and replication similar to those of killer viruses. (asm.org)
  • Packaging motor from double-stranded RNA bacteriophage phi12 acts as an obligatory passive conduit during transcription. (semanticscholar.org)
  • Some viruses like HIV have RNA as their genetic material that copies into DNA in a reverse transcription manner. (news-medical.net)
  • Sample exam questions: dna, transcription, it this a dna or rna virus? (jeffho.com)
  • RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. (viictr.org)
  • for example, the, bacteriophages are of four types: single stranded dna phages, single stranded rna phages , double stranded dna phages and double stranded rna phages. (jeffho.com)
  • virus replication to occur, a virus stranded dna, double-stranded rna and single-stranded rna viral replication will differ. (jeffho.com)
  • All viruses in Negarnaviricota are negative-sense, single-stranded RNA (-ssRNA) viruses. (wikipedia.org)
  • The biochemical and biophysical methods for the characterization of the recognition of RNA duplexes by the modified PNAs are described. (jove.com)
  • Included in these studies is identifying those intramolecular and intermolecular sequences in 1/2-sbsRNAs and mRNAs that bind STAU, defining STAU-containing RNA-binding complexes, and characterizing the physiological significance of the various STAU-mediated pathways. (rochester.edu)
  • It is shown here that transcriptional gene silencing accompanied by de novo methylation of a target promoter in plants can be triggered by a double‐stranded RNA containing promoter sequences. (embopress.org)
  • 2004. Relative gene-silencing efficiencies of small interfering RNAs targeting sense and antisense transcripts from the same genetic locus. (koreascience.or.kr)
  • Thus, STAU1 binding to 3'UTR inverted Alu elements, like removal of these elements by alternative RNA 3'-end cleavage and polyadenylation, obviates a PKR-mediated innate immune response to cytoplasmic 3'UTR inverted Alu elements. (rochester.edu)
  • Conversely, genetic loss of LGP 2 uncovers ds RNA ‐mediated RNA i albeit less strongly than complete loss of the IFN system. (embopress.org)
  • Like DNA, RNA can carry genetic information. (news-medical.net)
  • dADAR, a Drosophila double-stranded RNA-specific adenosine deaminase is highly developmentally regulated and is itself a target for RNA editing. (uniprot.org)
  • RNA‐directed DNA methylation (RdDM) was first discovered with a viroid system in plants ( Wassenegger, 2000 ). (embopress.org)
  • Such RNA enzymes are known as ribozymes, and they exhibit many of the features of a classical enzyme, such as an active site, a binding site for a substrate and a binding site for a cofactor, such as a metal ion. (news-medical.net)
  • Therefore, spatiotemporal patterns and levels of expression of hairpin RNAs are dependent on the Gal4 strain used. (nih.gov)
  • In addition, we showed that in contrast to DSB repair by single strand DNA (ssDNA) oligonucleotides (oligos), RNA templated DSB repair is not dependent on factors that are major players in DNA end resection. (gatech.edu)
  • Initiation of viral RNA-dependent RNA polymerization. (semanticscholar.org)
  • Like RecA, RAD51 catalyzes DNA strand exchange in an ATP-dependent manner ( Sung, 1994 ). (plantphysiol.org)
  • Double stranded RNA viruses replicate in the core capsid in the host cell cytoplasm and do depend as heavily on host polymerases as DNA viruses. (news-medical.net)
  • 17. The method of claim 12 in which the RNA is introduced within a body cavity of the organism and outside the target cell. (google.com)
  • Here, we dissected the IFN-α/β-stimulatory activity of different viral RNA species produced during picornavirus infection, both by RNA transfection and in infected cells in which specific steps of viral RNA replication were inhibited. (nih.gov)
  • Poliovirus-infected HeLa cells contain a small amount of an RNA that sediments slightly faster than 16S. (sciencemag.org)
  • Here, we investigated whether yeast cells can use transcript RNA as a template to repair a chromosomal DSB either directly or indirectly, if the RNA is converted first into a DNA copy, cDNA. (gatech.edu)
  • In this study, we report that model RNA, but not DNA, instigated robust cytokine and chemokine production from intact human coronary arteries containing both intrinsic vascular cells and resident/infiltrating leukocytes. (elsevier.com)
  • IFN-γ, a cytokine linked to atherosclerosis and graft arteriosclerosis, potentiated the inflammatory responses of intact arteries and cultured vascular smooth muscle cells (VSMCs) to polyinosinic: polycytidylic acid [poly(I:C)] and was necessary for inflammatory responses of VSMC to self-RNA derived from autologous cells. (elsevier.com)
  • Different constructs designed to produce double‐stranded promoter RNA in various ways were evaluated for their ability to induce gene silencing in tobacco and Arabidopsis . (embopress.org)
  • In addition, RAD51 is required for meiosis and its Arabidopsis ( Arabidopsis thaliana ) ortholog is important for normal meiotic homolog pairing, synapsis, and repair of double-stranded breaks. (plantphysiol.org)
  • Double-stranded RNA activates novel factors that bind to the interferon-stimulated response element. (asm.org)
  • Negative-strand RNA viruses constitute the phylum Negarnaviricota, in the kingdom Orthornavirae and realm Riboviria. (wikipedia.org)
  • Negative-strand RNA viruses are closely associated with arthropods and can be informally divided between those that are reliant on arthropods for transmission and those that are descended from arthropod viruses but can now replicate in vertebrates without the aid of arthropods. (wikipedia.org)
  • RNA Synthesis and Transfection. (pnas.org)
  • IFN-α/β production does not rely on plus-strand RNA synthesis and thus generation of the partially double-stranded replicative intermediate. (nih.gov)
  • This how DNA strands contain all the information required to replicate themselves. (coursehero.com)
  • A double stranded DNA virus enters the host nucleus before it begins to replicate. (news-medical.net)
  • The results also implicate double‐stranded RNA in directing DNA methylation. (embopress.org)
  • Transcriptional regulation of three double-stranded RNA segments of bacteriophage phi 6 in vitro. (semanticscholar.org)
  • We developed a system to detect HR between chromosomal DNA and transcript RNA in budding yeast, Saccharomyces cerevisiae. (gatech.edu)
  • For example, introns are spliced out of pre-mRNA by spliceosomes, which contain several small nuclear RNAs (snRNA). (news-medical.net)
  • For example, the chromosome of some small viruses have single-stranded, not double-stranded, rna exhibits extensive double-helical double-stranded rna viruses. (jeffho.com)
  • Is the Subject Area "Small interfering RNA" applicable to this article? (plos.org)
  • This RNA is less dense than viral RNA and resists digestion by ribonuclease. (sciencemag.org)
  • Interestingly, in the absence of Ribonuclease H1 and H2 (RNases H1 and H2), we could detect DSB repair even in conditions that strongly inhibit cDNA formation, suggesting direct DSB repair by transcript RNA. (gatech.edu)
  • Furthermore, the capability to inhibit AP-1 promoter was mapped in the effector domain, since RNA binding domain alone lost its ability to inhibit this promoter activation. (lancs.ac.uk)
  • These results underscore the importance of the effector domain in inhibiting AP-1 promoter activation, and the biological function of the effector domain in stabilizing the RNA binding domain. (lancs.ac.uk)
  • Enzymes called DNA helicase unwind the coiled double helix of DNA, beginning at the point called the replication fork. (coursehero.com)
  • The replication of the positive sense rna viruses occurs through the double-stranded rna intermediate. (jeffho.com)
  • We proved that transcript RNA can repair a DSB indirectly, via cDNA. (gatech.edu)
  • In contrast to DSB repair by cDNA, the direct DSB repair by transcript RNA is more efficient in the cis than in the trans system, despite the higher abundance of the transcript in the trans system. (gatech.edu)