• Reduced activity of the interferon-induced double-stranded RNA-dependent protein kinase during a heat shock stress. (wikidata.org)
  • Previous research has shown that infection with coronaviruses activates an innate immune response upon sensing of viral RNA by interferon-induced with helicase C domain 1 (IFIH1), also known as MDA5. (frontiersin.org)
  • Relatively simple, synthetic, double-stranded RNAs can be powerful viral pathogen-associated molecular pattern (PAMP) mimics, inducing a panoply of antiviral and antitumor responses that act at multiple stages of host defense. (elsevierpure.com)
  • DDX58/RIG-I, a sensor of cytoplasmic viral RNA and toll-like receptors (TLR) 3, 7, and 8, which bind RNA in endosomes, are conserved in pangolins. (frontiersin.org)
  • Cellular 5'-3' mRNA exonuclease Xrn1 controls double-stranded RNA accumulation and anti-viral responses. (nih.gov)
  • The etiological agent, CSF virus (CSFV), is an enveloped virus with a positive-sense, single-stranded RNA genome, classified as a member of the genus Pestivirus within the family Flaviviridae (Becher et al. (usda.gov)
  • Therefore, the conversion of the DSB ends from double-stranded to single-stranded DNA, which is necessary to initiate DSB repair by homologous recombination, is responsible for loss of transcription around a DSB in S. cerevisiae . (elifesciences.org)
  • These single-stranded DNA 'tails' are then free to interact with an intact copy of the same DNA sequence from elsewhere in the cell's nucleus, which is used as a guide when repairing the damage. (elifesciences.org)
  • Instead, the experiments indicate that it is the resection of the DNA around a double-strand break to form single-stranded tails that inhibits transcription in budding yeast. (elifesciences.org)
  • Identification of a 90-kDa polypeptide which associates with adenovirus VA RNAI and is phosphorylated by the double-stranded RNA-dependent protein kinase. (wikidata.org)
  • The double stranded RNA-activated protein kinase induced by interferon: dsRNA-PK. (wikidata.org)
  • The double-stranded (ds) RNA-activated protein kinase, DAI (also known as PKR), contains an RNA-binding domain comprising two tandem repeats of a motif, the dsRBM, which is shared with a number of other proteins that interact with structured RNAs. (cshl.edu)
  • We have expressed the entire domain and the first copy of the motif in Escherichia coli and purified the two proteins, p20 and p10, to apparent homogeneity in order to study their interactions with RNA and with the intact kinase enzyme. (cshl.edu)
  • Emerging evidence indicate that the mammalian checkpoint kinase ATM induces transcriptional silencing in cis to DNA double-strand breaks (DSBs) through a poorly understood mechanism. (elifesciences.org)
  • Both p20 and p10 bound preferentially to structured RNA molecules. (cshl.edu)
  • The proteins involved in homologous recombination have to work around other processes that go on inside the nucleus, such as the transcription of DNA in genes into RNA molecules. (elifesciences.org)
  • For short templates we recommend to increase in template concentration, polymerase concentration and reaction time, since transcription of small RNAs is largely dependent on the number of initiation events. (neb.com)
  • 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)
  • Likewise, Z-DNA-binding protein (ZBP1), which senses both Z-DNA and Z-RNA, has been lost during the evolution of pangolins. (frontiersin.org)
  • Here we describe prime editing, a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit. (nature.com)
  • RNA-guided human genome engineering via Cas9. (nature.com)
  • In this study, we identified three efficient target genes (β‐ Actin , SRP54 , and SNAP ) for RNAi using in vitro double‐stranded RNAs (dsRNAs) fed to HV, and found that dsRNAs targeting β‐ Actin messenger RNA ( dsACT ) induced more potent RNAi than those targeting the other two genes. (jipb.net)
  • Here, we performed a comparative genomics study of RNA sensor genes in three species of pangolins. (frontiersin.org)
  • Previous research has reported that forming a double-strand break in the DNA reduces the levels of transcription for the genes that surround the break, but it was not clear how this occurred. (elifesciences.org)
  • In mammalian cells, inhibiting the transcription of genes around a double-strand DNA break depends on a signaling pathway that is activated whenever DNA damage is detected. (elifesciences.org)
  • One of the next challenges will be to see if the resection process makes any contribution to changes in the transcription of genes that surround a double-strand break in mammals as well. (elifesciences.org)
  • RNA interference (RNAi) has emerged as a powerful technology for pest management. (jipb.net)
  • RNA Interference-mediated Silencing of Phytochelatin Synthase Gene Reduce Cadmium Accumulation in Rice Seeds [J]. J Integr Plant Biol. (jipb.net)
  • Sodium Stress in the Halophyte Thellungiella halophila and Transcriptional Changes in a thsos1-RNA Interference Line [J]. J Integr Plant Biol. (jipb.net)
  • RNA interference is an evolutionary conserved gene regulatory mechanism that can be used by introducing exogenous synthetic double-stranded RNAs, so called small interfering RNA (siRNA). (lu.se)
  • However, a key challenge in translating siRNA into the clinic is the inefficacy to deliver siRNA across the plasma membrane, but most importantly, to escape the endosomal system and reach the cytosol where they can interact with the RNA interference machinery. (lu.se)
  • 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)
  • DNA double-strand breaks (DSBs) are particularly dangerous for cells, since their inefficient or inaccurate repair can result in deletions and chromosomal translocations that can lead to cancer and/or severe developmental abnormalities in humans. (elifesciences.org)
  • Originally, it was thought that only intermediate and late gene transcription produced double-stranded (ds) RNA to activate PKR during vaccinia virus (VACV) infection. (elsevierpure.com)
  • Long ds ACT stably accumulated to up to 0.7% of the total cellular RNA in the transplastomic plants, at least three orders of magnitude higher than in the nuclear transgenic plants. (jipb.net)
  • Translational control by the Epstein-Barr virus small RNA EBER-1. (wikidata.org)
  • Identification of phlebovirus and arenavirus RNA sequences that stall and repress the exoribonuclease XRN1. (nih.gov)
  • This mechanism requires enzymes to eat away at the end of one of the DNA strands on each side of the double-strand break. (elifesciences.org)
  • We performed more than 175 edits in human cells, including targeted insertions, deletions, and all 12 types of point mutation, without requiring double-strand breaks or donor DNA templates. (nature.com)
  • Is the Subject Area "Non-coding RNA" applicable to this article? (plos.org)
  • Description: RNA profiling data sets generated by the Mouse ENCODE project. (nih.gov)
  • Kosicki, M., Tomberg, K. & Bradley, A. Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements. (nature.com)
  • Breaks that form across both strands in a DNA double helix are considered the most dangerous type of DNA damage, and can cause a cell to die or become cancerous if they are not repaired accurately. (elifesciences.org)
  • Homologous recombination' is one of the main mechanisms used by cells to repair DNA double-strand breaks. (elifesciences.org)
  • RNA isolated from infected RK13 or HeLa cells maintained PKR-activating properties only when dsRNA was present. (elsevierpure.com)
  • This can be avoided by following some simple precautions: 1) always wear gloves when working with RNA, 2) use either a dedicated set of pipettors for RNA work or aerosol-resistant (barrier) pipette tips, 3) use ultrapure water (Milli-Q or equivalent) and autoclave all solutions if possible, and 4) use disposable plasticware instead of glassware whenever possible. (neb.com)
  • The aim of this thesis was to develop novel methods to study the process of endosomal escape and cytosolic delivery of RNA. (lu.se)
  • Double-stranded RNA (dsRNA) has been shown to trigger sequence-specific gene silencing in a wide variety of organisms, including plant, nematode and invertebrate species. (nih.gov)
  • In nematodes, they found that very small amounts of double-stranded RNA (dsRNA) complementary to a particular gene could suppress the expression of that gene by virtually eliminating its messenger RNA (mRNA). (medscape.com)
  • This dsRNA-mediated silencing proved to be much more potent than that caused by the single-stranded, antisense reagents that had long been used by scientists. (medscape.com)
  • The role of ADARs is to deaminate adenosine to inosine non-specifically in long double-stranded RNA (dsRNA) or site-specifically in transcripts. (biomedcentral.com)
  • Flaviviruses are a large group of positive strand RNA viruses transmitted by arthropods that include many human pathogens such as West Nile virus (WNV), Japanese encephalitis virus (JEV), yellow fever virus, dengue virus, and tick-borne encephalitis virus. (mdpi.com)
  • Positive-strand RNA viruses, the largest genetic class of viruses, include numerous important pathogens such as Zika virus. (elifesciences.org)
  • RNA replication on expanded, rearranged cellular membranes is universal among positive-strand RNA viruses and thus presents a target for broadly applicable antiviral therapies. (elifesciences.org)
  • [ 7 ] At approximately 21 nucleotides in length and containing 3' overhangs, siRNAs possess both a guide (or antisense) strand that is complementary to the target mRNA, and a passenger strand. (medscape.com)
  • RISC contains the endonuclease Argonaute 2 (AGO2), which cleaves bound mRNA provided that it is perfectly complementary to the guide strand. (medscape.com)
  • [ 15 ] The cleaved mRNA is rapidly destroyed, leaving the RISC-guide strand complex available for additional cycles of mRNA binding and cleavage (Figure 1, purple arrows denote siRNA pathway). (medscape.com)
  • In the first step of making a protein from a gene, another type of RNA called messenger RNA (mRNA) is formed and acts as the blueprint for protein production. (medlineplus.gov)
  • We believe that the success of mRNA COVID vaccines will propel a sooner-than-expected wave of RNA innovation in the industry. (bcg.com)
  • and help to spatially segregate the viral RNA genome's competing functions as an mRNA for viral protein synthesis, a template for viral RNA synthesis, and a substrate for encapsidation. (elifesciences.org)
  • Transfecting the cells with a small interfering RNA (siRNA) designed to degrade the messenger RNA (mRNA) for CD4 indeed blocked HIV infection by 4- to 10-fold. (the-scientist.com)
  • Encouraged by these results, we used RNA silencing to target an HIV gene that encodes for the viral capsid, and found that we could knock down both the host mRNA and the viral mRNA within the host cell. (the-scientist.com)
  • sfRNA is a product of incomplete degradation of genomic RNA by the cell 5'-3' exoribonuclease XRN1 which stalls at highly ordered secondary RNA structures at the beginning of the 3'UTR. (mdpi.com)
  • 12. Chemically modified symmetric and asymmetric duplex RNAs: an enhanced stability to nuclease degradation and gene silencing effect. (nih.gov)
  • This transcript may also stabilize mRNAs by blocking degradation by staufen double-stranded RNA binding protein 1. (nih.gov)
  • This inhibition has been shown to be superior to single-stranded antisense oligonucleotides and opens the possibility of the use of dsRNAs as reverse genetic and therapeutic tools in mammalian cells. (nih.gov)
  • 15. A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells. (nih.gov)
  • My curiosity was thus piqued when 3 years later Carl Novina, a postdoc in Phillip Sharp's lab whom I had known when he was a graduate student at Tufts, came to me with the still-unpublished news that RNA silencing also functions in mammalian cells. (the-scientist.com)
  • TRBP, trans-activation-responsive RNA binding protein. (medscape.com)
  • The encoded protein is a double-stranded RNA binding protein that functions as the non-catalytic subunit of the microprocessor complex. (nih.gov)
  • This protein is required for binding the double-stranded RNA substrate and facilitates cleavage of the RNA by the ribonuclease III protein, Drosha. (nih.gov)
  • 1. Lipid-conjugated 27-nucleotide double-stranded RNAs with dicer-substrate potency enhance RNAi-mediated gene silencing. (nih.gov)
  • These viruses replicate their RNA genomes in novel, membrane-bounded mini-organelles, but the organization of viral proteins and RNAs in these compartments has been largely unknown. (elifesciences.org)
  • Many insects naturally produce these double-stranded RNA molecules as an immune response to infections by viruses, bacteria or fungi. (newscientist.com)
  • When the team sequenced the natural RNAs in the jellies, they found RNAs corresponding to ten viruses, suggesting that bees start making and sharing disease-targeting RNAs when infections strike. (newscientist.com)
  • LncRNA small nucleolar RNA host gene 5 inhibits trophoblast autophagy in preeclampsia by targeting microRNA-31-5p and promoting the transcription of secreted protein acidic and rich in cysteine. (nih.gov)
  • Specific Inhibition of Gene Expression by Small Double-Stranded RNAs in Invertebrate and Vertebrate Systems," Proc. (nih.gov)
  • The discovery of this RNA-based gene-silencing in organisms as diverse as plants, worms and humans suggested that cells must possess evolutionarily conserved machinery that mediates the process. (medscape.com)
  • The ADAR1 gene was found to encode three double-stranded-RNA binding domains (dsRBDs) and a deaminase domain with zinc-binding motifs (Figure 1 ), similar to those of zinc-dependent cytosine deaminases and to the cytosine-to-uracil RNA-editing enzyme APOBEC1. (biomedcentral.com)
  • 14. SiRNAs conjugated with aromatic compounds induce RISC-mediated antisense strand selection and strong gene-silencing activity. (nih.gov)
  • This gene represent a snoRNA host gene and produces a long non-coding RNA. (nih.gov)
  • This RNA may regulate gene expression by acting as a sponge for microRNAs. (nih.gov)
  • I was intrigued and perplexed by the paper: how could a double-stranded RNA possibly silence gene expression? (the-scientist.com)
  • 10. Competition potency of siRNA is specified by the 5'-half sequence of the guide strand. (nih.gov)
  • When the small interfering RNAs (siRNA) were taken up by liver cells, they degraded the RNA message for the Fas receptor, preventing even the most deadly and acute liver damage. (the-scientist.com)
  • Once in the cytoplasm, dsRNAs still joined by a loop, whether derived from nuclear processing events or from exogenous delivery as synthetic Dicer substrates, require processing by TRBP-Dicer (3), resulting in separation into two strands. (medscape.com)
  • All dsRNAs converge in loading the guide strand into RISC (4), whereas endogenous miRNAs mostly lead to translational repression, and exogenous dsRNAs to target cleavage. (medscape.com)
  • Synthesis of the dsDNA template and transcription of RNA occur in a single reaction, resulting in the generation of a functional sgRNA. (neb.com)
  • Substrates of ADARs include viral RNAs and endogenous transcripts. (rupress.org)
  • Viral RNAs are frequently edited promiscuously, but can also be edited specifically affecting only a few residues. (rupress.org)
  • Type I interferons (IFNs) are a group of antiviral cytokines that are induced during viral infection by viral-replication products, such as double-stranded (ds)RNA. (nature.com)
  • The structural organization of viral RNAs and proteins at such membrane-associated sites of RNA replication has been largely unknown. (elifesciences.org)
  • Adenosine deaminases that act on RNA (ADARs) * are a family of RNA-editing enzymes that catalyze the hydrolytic deamination of adenosines to inosines in a diverse group of mostly double-stranded RNA substrates. (rupress.org)
  • Structurally, all ADARs possess a conserved deaminase domain in their COOH terminus required for enzymatic activity as well as one or several copies of the double-stranded RNA-binding domain (dsRBD) in their central region. (rupress.org)
  • Adenosine deaminases acting on RNA (ADARs) were discovered as a result of their ability extensively to deaminate adenosines in any long double-stranded RNA, converting them to inosines. (biomedcentral.com)
  • It appears that ADARs evolved from a member of another family, adenosine deaminases acting on tRNAs (ADATs), by steps including fusion of two or more double-stranded-RNA binding domains to a common type of zinc-containing adenosine-deaminase domain. (biomedcentral.com)
  • MicroRNAs are short lengths of RNA, a chemical cousin of DNA. (medlineplus.gov)
  • Some of these noncoding RNAs, called microRNAs because of their small size, interfere with protein expression by chopping up protein. (the-scientist.com)
  • Target-specific oligos (or EnGen sgRNA Control Oligo, S. pyogenes) are mixed with the EnGen 2X sgRNA Reaction Mix (NTPs, dNTPs, S. pyogenes Cas9 Scaffold Oligo), 0.1 M DTT and the EnGen sgRNA Enzyme Mix (DNA and RNA polymerases) at room temperature. (neb.com)
  • RNA treatments dramatically expand the range of druggable targets for illnesses and conditions, including previously out-of-reach intracellular proteins. (bcg.com)
  • What's more, bees produce special proteins that bind to RNAs to protect the molecules and prevent them from breaking down. (newscientist.com)
  • That puzzling finding began to make sense when we realized that we were missing a big part of the picture: a lot of DNA is transcribed into RNA but never into proteins. (the-scientist.com)
  • 19. Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. (nih.gov)
  • The RNA-editing enzyme adenosine deaminase that acts on RNA (ADAR1) deaminates adenosines to inosines in double-stranded RNA substrates. (rupress.org)
  • The crRNA, or CRISPR RNA sequence contains approximately 20 nucleotides of homology complementary to the strand of DNA opposite and upstream of a PAM (Protospacer Adjacent Motif) (NGG) sequence. (neb.com)
  • While RNA still faces long-term safety and efficacy (as well as likely cost) challenges, recent advances suggest material technology improvements are coming soon. (bcg.com)
  • 8. Detection of long and short double-stranded RNAs. (nih.gov)
  • Many crowns were associated with long cytoplasmic fibrils, likely to be exported progeny RNA. (elifesciences.org)
  • These sequences have been adapted for use in the lab by combining the tracrRNA and crRNA into one long single guide RNA (sgRNA) (1) species capable of complexing with Cas9 to recognize and cleave the target DNA. (neb.com)
  • In all cases, the amount of added template DNA should not exceed 2 µg per 40 µl reaction, as RNA yields will not be higher at template concentrations greater than this. (neb.com)
  • This is the first time that individuals of the same species have been shown to exchange RNA in this way, says Maori. (newscientist.com)
  • We used cryo-electron tomography to reveal many previously unrecognized features of Flock house nodavirus (FHV) RNA replication compartments. (elifesciences.org)
  • Here, we demonstrate that chromosomal association depends solely on the three double-stranded RNA-binding domains (dsRBDs) found in the central part of ADAR1, but not on the Z-DNA-binding domain in the NH 2 terminus nor the catalytic deaminase domain in the COOH terminus of the protein. (rupress.org)
  • Now investigating this further, Maori and his team found that bees pass RNAs on to other bees by adding them to the worker and royal jellies that they secrete to feed larvae. (newscientist.com)
  • Here, we review the recent advances concerning the complex interaction of viroids with the host's RNA silencing machinery, evaluate past and present antiviroid approaches, and finally suggest alternative strategies that could potentially be employed in the future in order to achieve transgenic and non-transgenic viroid-free plants. (mdpi.com)
  • These spherular invaginations of outer mitochondrial membranes are packed with electron-dense RNA fibrils and their volumes are closely correlated with RNA replication template length. (elifesciences.org)
  • Such challenges include making RNA more recognizable by the human immune system and developing molecular delivery vehicles for specific tissues. (bcg.com)
  • Bees may also use RNAs to prepare future generations for the specific environment they will face. (newscientist.com)
  • All members in this genus tested so far are shown to produce a unique subgenomic flavivirus RNA (sfRNA) derived from the 3' untranslated region (UTR). (mdpi.com)
  • RNA silencing-based technologies seem to be a promising tool in this direction. (mdpi.com)
  • Several attributes, including a fit-for-purpose molecular design and functional versatility , make RNA one of the most promising new treatment technologies. (bcg.com)
  • Several attributes make RNA one of the most promising new treatment technologies. (bcg.com)
  • To address these questions, we turned to flock house virus (FHV), a well-studied, model positive-strand RNA virus in the nodavirus family. (elifesciences.org)