• Hepatitis C RNA: Testing for HCV RNA by reverse-transcriptase ¬polymerase-chain reaction (RT-PCR) amplification of the 5' noncoding region was performed on anti-HCV positive samples. (cdc.gov)
  • RNA polymerase transcription initiation sites are largely unknown in Caenorhabditis elegans. (nih.gov)
  • Directed elongation from an upstream enhancer toward a downstream gene could potentially deliver RNA polymerase II to a proximal promoter, or alternatively might function directly as a distal promoter. (nih.gov)
  • The nomenclature of different promoter-associated RNA polymerase II (Pol II) species is explicitly defined in an effort to provide consistency in future literature. (nature.com)
  • Recent years have witnessed a sea change in our understanding of transcription regulation: whereas traditional models focused solely on the events that brought RNA polymerase II (Pol II) to a gene promoter to initiate RNA synthesis, emerging evidence points to the pausing of Pol II during early elongation as a widespread regulatory mechanism in higher eukaryotes. (nature.com)
  • In this study, for simplicity, we refer to intergenic lncRNAs as those that are transcribed by RNA-polymerase II, 5′ end capped and polyadenylated. (biomedcentral.com)
  • All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. (osti.gov)
  • To investigate the molecular mechanisms involved we determined the extent of interaction of RNA polymerase with the promoter of the tyrT stable RNA gene. (dundee.ac.uk)
  • A mutant tyrT promoter, tyrTp27, is protected more extensively, RNA polymerase interactions extending to at least ∼-130. (dundee.ac.uk)
  • In bacterial RNA polymerase (RNAP), the bridge helix and switch regions form an intricate network with the catalytic active centre and the main channel. (houstonmethodist.org)
  • AsiA simultaneously occupies the surface of region 4 that ordinarily contacts core RNA polymerase (RNAP), suggesting that an AsiA-bound sigma70 may also undergo conformational changes in the context of the RNAP holoenzyme. (rcsb.org)
  • 87(5): 1663-1667] Specifically, the investigators started by priming whole cerebellar RNA with a synthetic oligonucleotide containing a T7 RNA polymerase promoter sequence. (genomicglossaries.com)
  • After second- strand cDNA synthesis, T7 RNA polymerase was used to generate aRNA. (genomicglossaries.com)
  • Among 20 laboratories testing Module A, 17 (85%) correctly detected DENV RNA by reverse transcription polymerase chain reaction (RT-PCR), 18 (90%) correctly determined serotype and 19 (95%) correctly identified CHIKV by RT-PCR. (who.int)
  • RNA-binding proteins (RBPs) exert a broad range of biological functions. (nature.com)
  • Only 60% of yeast and 73% of the human RBPs have functions assigned to RNA biology or structural motifs known to convey RNA binding, and many intensively studied proteins surprisingly emerge as RBPs (termed 'enigmRBPs'), including almost all glycolytic enzymes, pointing to emerging connections between gene regulation and metabolism. (nature.com)
  • RNA-binding proteins (RBPs) mediate pivotal cellular functions such as RNA transport, degradation or translation and represent key effectors of post-transcriptional gene regulation. (nature.com)
  • We show that this conserved RNA interactome harbours many proteins without previously assigned roles in RNA biology (enigmRBPs), including surprisingly many metabolic enzymes. (nature.com)
  • After cell lysis, polyadenylated RNAs were captured on oligo d(T) beads followed by stringent washes to remove non-crosslinked proteins. (nature.com)
  • As a means to identify cellular RNA targets for these proteins, we devised combinatorial shape libraries representing naturally derived 3' untranslated regions and were able to select a structurally related subset of transcripts that bound to Hel-N1. (duke.edu)
  • This approach provides a means to gain access to novel genes expressed in various cell types by partitioning mRNAs containing common sequence elements using RNA-binding proteins. (duke.edu)
  • Messenger RNA is a kind of intermediary that tells the body how to convert the instructions contained in the genome into actual proteins. (cdc.gov)
  • In infected cells , its positive-sense RNA genome is translated into polyproteins that are subsequently processed into four nonstructural proteins (nsP1 to 4), the virus -encoded subunits of the RNA replicase . (bvsalud.org)
  • However, for RNA replication , interactions between nsPs and host proteins are also needed. (bvsalud.org)
  • CHIKV replication depends on the ability of its replicase proteins to interact with host cell factors, and a better understanding of host cell factor roles in viral infection will increase our understanding of CHIKV RNA replication and provide new strategies for viral infection attenuation. (bvsalud.org)
  • When these genes are expressed to make proteins, they are first copied into RNA. (newscientist.com)
  • By varying what RNA regions are stitched together, the same gene can provide multiple templates for slightly altered proteins. (newscientist.com)
  • Those included antisense RNAs and UTR regions. (wikipedia.org)
  • We show that the enzyme can protect from DNAase I digestion a region of at least 85 bp of the wild-type tyrT promoter and only ∼62 bp of the lacUV5 mRNA promoter, the protected region extending on the antisense strand to ∼65 and 42 bp respectively upstream of the transcription startpoint. (dundee.ac.uk)
  • Interestingly, ZNFX1 antisense RNA 1 (ZFAS1) could abolish its tumor suppressor effect by binding microRNA (miR)-150, while miR-150 could inhibit the invasion of hepatic carcinoma cells by inhibiting zinc finger E-box binding homeobox 1 (ZEB1) and matrix metalloproteinases (MMP)14 and MMP16 ( 10 ). (spandidos-publications.com)
  • Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. (genomicglossaries.com)
  • Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes. (genomicglossaries.com)
  • More specifically, antisense oligonucleotides that are useful as reagents for target validation , or as drugs, are engineered molecules that differ from natural RNA but that have a base sequence that is recognized as being complementary to a very specific mRNA sequence. (genomicglossaries.com)
  • The integrity of each RNA sample as indicated by intact ribosomal RNA is verified by denatured agarose gel electrophoresis. (delos.info)
  • Together, these methods predict the existence of multiple, often juxtaposed stem-loops that are found in all HCV genotypes throughout both regions, as well as several strikingly conserved single-stranded regions, one of which coincides with a region of the genome to which ribosomal access is required for translation initiation. (ox.ac.uk)
  • The initial PCR reaction amplifies a region of the HCV genome (External primers). (cdc.gov)
  • In a historic first, a group of CDC laboratory and bioinformatics scientists became the first to directly sequence an RNA genome. (cdc.gov)
  • For decades, scientists who wanted to research the genome of RNA viruses, such as influenza, had to do so using an indirect and time-consuming method that involved first converting the single-stranded RNA into double-stranded DNA. (cdc.gov)
  • The new method described in this study has the potential to allow researchers to decode the genome of an RNA virus with greater detail (and less distortion) than ever before. (cdc.gov)
  • Now that Keller et al have managed to directly sequence RNA for the first time, the group hopes to find details of the influenza A virus' genome that are otherwise hidden and extremely difficult to detect. (cdc.gov)
  • At least 50,000 lncRNAs are expressed from intergenic regions of the human genome, more than twice the number of protein-coding genes [ 5 ]. (biomedcentral.com)
  • Comparative analysis of RNA-Seq data and the genome sequence did not provide evidence for RNA editing in C. graminicola . (biomedcentral.com)
  • There is accumulating evidence from bioinformatic studies that hepatitis C virus (HCV) possesses extensive RNA secondary structure in the core and NS5B-encoding regions of the genome. (ox.ac.uk)
  • The configuration and genetic variability of many of these other NS5B and core structures is perhaps more consistent with their involvement in genome-scale ordered RNA structure, a structural configuration of the genomes of many positive-stranded RNA viruses that is associated with host persistence. (ox.ac.uk)
  • ArciTect™ tracrRNA is a trans-activating CRISPR RNA (crRNA), one of two RNA components required to make a guide RNA (gRNA) for CRISPR-Cas9 genome editing. (stemcell.com)
  • Find regions of similarity between this sequence and other sequences using BLAST. (nih.gov)
  • Finds sub-sequences or patterns in the sequence and highlights the matching regions. (nih.gov)
  • Selection of RNA targets from randomized combinatorial libraries yielded (A+U)-rich consensus sequences for both Hel-N1 and Hel-N2. (duke.edu)
  • Keller said that messenger RNA has a tail end that is comprised of a sequences of "A's. (cdc.gov)
  • The third class of thermosensing is based on the temperature-dependent conformation of specific RNA sequences, which are termed RNA-thermometer (RNAT). (springer.com)
  • These sequences typically include the 5′-untranslated region in mRNA including the ribosome binding site (Shine-Dalgarno sequence) and in some cases the start codon (Klinkert and Narberhaus 2009 ). (springer.com)
  • Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods. (ox.ac.uk)
  • A total 3 short hairpin RNA (sh)‑lncRNA XIST sequences, overexpression vector (oe)‑lncRNA XIST, microRNA (miR)‑320a mimic, miR‑320a inhibitor, PIK3CA inhibitor, and their corresponding controls were transfected in hepatic carcinoma cells. (spandidos-publications.com)
  • RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. (genomicglossaries.com)
  • RNA is ideal for Northern blotting, ribonuclease protection assay, SI nuclease assay, RT-PCR/Q-PCR/RACE analysis, cDNA synthesis, RNA differential display, microRNA studies, and purification of mRNA for library construction. (delos.info)
  • DksA does not seem to significantly affect RNAP binding to a pre-melted promoter DNA but affects extensively activity at the stage of initial RNA synthesis on σ 54 -regulated promoters. (houstonmethodist.org)
  • By targeting conserved residues in Escherichia coli RNAP, we are able to show that functions of these regions are differentially required during σ 70 -dependent and the contrasting σ 54 -dependent transcription activations and thus potentially underlie the key mechanistic differences between the two transcription paradigms. (houstonmethodist.org)
  • Long non-coding (lnc)RNAs play important roles in the development, differentiation, proliferation and apoptosis of cells ( 6 , 7 ). (spandidos-publications.com)
  • Stored sera from a population of individuals, who tested positive for hepatitis C infection as part of the NHANES III (1988-1994) survey, were analyzed for the presence of hepatitis C virus (HCV) RNA. (cdc.gov)
  • Currently, there are three basic types of tests to determine if an individual has been infected with SARS-CoV-2: viral nucleic acid (RNA) detection, viral antigen detection, and detection of antibodies to the virus. (medscape.com)
  • It can be accessed online at www.helmholtz-hiri.de/en/datasets/enterococcus through an instance of the genomic viewer JBrowse. (frontiersin.org)
  • These novel bioinformatic methods have been combined with enzymic mapping of RNA transcripts from the core and NS5B regions to precisely delineate the RNA structures that are present in these genomic regions. (ox.ac.uk)
  • One capability of the nanopore sequencer is to sequence messenger RNA. (cdc.gov)
  • It was this messenger RNA workflow that was modified to sequence influenza viral RNA. (cdc.gov)
  • Changes in hepatic Cyp7a1 messenger RNA (mRNA) correlated with those of Cyp24a1 (a Vdr target gene) and inversely with Shp mRNA, but not ileal Fgf15 mRNA. (nih.gov)
  • The HCV RNA was isolated and sequenced either to determine the genotype of the isolated virus or to determine the viral quasispecies diversity within an infected individual. (cdc.gov)
  • The viral vectors also need to maintain transgene expression at an appropriate level and duration to efficiently deliver the therapeutic effect, which is measured by extracting and quantifying RNA through similar methods. (beckman.com)
  • Total RNA is routinely extracted from single healthy normal donor using the powerful classical guanidine isothiocyanate-phenol:chloroform extraction method which allows the rapid isolation of total RNA including microRNAs. (delos.info)
  • Total RNA sample is routinely provided in RNase-free water at a concentration of 1 mg/ml and shipped on dry ice. (delos.info)
  • In the recent past, the presence and function of a ROSE-like RNA-thermometer located in the 5′UTR of the rhamnosyltransferase genes rhlAB has been reported in wild type P. aeruginosa . (springer.com)
  • For this purpose, the non-pathogenic production host P. putida KT2440 containing the rhlAB genes with the native P. aeruginosa 5′-UTR region was used. (springer.com)
  • We successfully employed deep sequencing RNA-Seq data in combination with an elaborate bioinformatics strategy in order to identify novel genes, incorrect gene models and mechanisms of transcript processing in the corn anthracnose fungus C. graminicola . (biomedcentral.com)
  • Analyzing bacteria in late exponential phase, we capture ~40% ( E. faecalis ) and 43% ( E. faecium ) of the annotated protein-coding genes, determine 5′ and 3′ UTR (untranslated region) length, and detect instances of leaderless mRNAs. (frontiersin.org)
  • A better understanding of how these species cause disease and spread antibiotic resistance requires a knowledge of how its genes are controlled, on both the DNA and the RNA level. (frontiersin.org)
  • The three-dimensional structure of an AsiA/region 4 complex reveals that the C-terminal alpha helix of region 4 is unstructured, while four other helices adopt a completely different conformation relative to the canonical structure of unbound region 4. (rcsb.org)
  • The technique uses SPRI bead-based technology that selectively binds DNA and RNA to the beads and effectively separates DNA and RNA independently. (beckman.com)
  • A complementary RNA sequence that binds to a naturally occurring (sense) mRNA molecule, thus blocking its translation. (genomicglossaries.com)
  • The technology behind our work involves detecting a disease signature of RNA molecules called microRNA which can be isolated from small biological vesicles called 'exosomes' that travel in the bloodstream. (edu.au)
  • Despite their critical implication in worldwide public healthcare, essential and available resources such as deep transcriptome annotations remain poor, which also limits our understanding of post-transcriptional control small regulatory RNA (sRNA) functions in these bacteria. (frontiersin.org)
  • We are also studying other noncoding RNA fragments such as UTRs, and are generally interested in both the process of transcription and in the post-transcriptional fate of RNA molecules. (weizmann.ac.il)
  • To address the second, we investigated RNAs bound by the metabolic enzyme hydroxysteroid dehydrogenase 17-β 10 (HSD17B10). (nature.com)
  • We also determined the RNA targets of an RNA-binding mitochondrial enzyme and show its specificity in RNA binding. (nature.com)
  • RNA which contains an intron sequence that has an enzyme- like catalytic activity. (genomicglossaries.com)
  • These two classes of 5′ capped and polyadenylated RNA transcripts are indistinguishable with regard to their length, number of exons or transcriptional orientation relative to their closest neighboring gene. (biomedcentral.com)
  • Based on the nucleotide sequence information of transcripts, we identified 819 novel transcriptionally active regions (nTARs) and revised 906 incorrectly predicted gene models, including revisions of exon-intron structure, gene orientation and sequencing errors. (biomedcentral.com)
  • Scholars@Duke publication: Selection of a subset of mRNAs from combinatorial 3' untranslated region libraries using neuronal RNA-binding protein Hel-N1. (duke.edu)
  • Hel-N1 has been shown to bind in vitro to 3' untranslated regions of mRNAs encoding c-myc, c-fos, granulocyte/macrophage colony-stimulating factor, and transcriptional repressor, Id. (duke.edu)
  • Long noncoding RNAs (lncRNAs) contain at least 200 bases, and are molecularly identical to mRNAs. (weizmann.ac.il)
  • With maximum values of 0.23 g/(g h) at 37 °C, this constitutes a more than 60% increase compared to the production rate of 0.14 g/(g h) at the growth optimum of 30 °C. Interestingly however, control experiments unveiled that besides the regulatory effect of the RNA-thermometer, multiple metabolic effects may contribute equally to the observed increase in production rate. (springer.com)
  • We speculate that by coupling RNA processing to the status and activity of Pol II itself, the cell ensures that nascent RNA is properly protected from degradation and efficiently matures into a functional mRNA. (nature.com)
  • Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. (nature.com)
  • However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. (osti.gov)
  • The structures reveal that-for both the primary σ-factor and extracytoplasmic (ECF) σ-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA-the "σ-finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from ~5 nt to ~10 nt. (osti.gov)
  • We subclassified intergenic lncRNAs according to chromatin status at transcriptional initiation regions, defined by relative levels of histone H3K4 mono- and trimethylation. (biomedcentral.com)
  • Here we address two important, and incompletely answered, questions concerning the origins (transcriptional initiation regions (TIRs)) and classification of intergenic lncRNAs. (biomedcentral.com)
  • By using strand-specific RNA-seq analysis and in silico sRNA predictions 137 small RNAs candidates were identified in Pectobacterium atrosepticum under starvation conditions. (wikipedia.org)
  • G3BP/Rin-Binding Motifs Inserted into Flexible Regions of nsP2 Support RNA Replication of Chikungunya Virus. (bvsalud.org)
  • Strikingly, the majority of initiation events occur in regions with enhancer-like chromatin signatures. (nih.gov)
  • We characterized the landscape of RNA Pol II transcription initiation, identifying 73,500 distinct clusters of initiation. (nih.gov)
  • In this paper, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "σ-finger" of the bacterial transcription initiation factor σ. (osti.gov)
  • A program was developed (STRUCTUR_DIST) that analyses multiple rna-folding patterns predicted by mfold to determine the evolutionary conservation of predicted stem-loop structures and, by a new method, to analyse frequencies of covariant sites in predicted RNA folding between HCV genotypes. (ox.ac.uk)
  • Links in the FEATURES table will also highlight the corresponding region of the sequence. (nih.gov)
  • Finds sub-sequence or patterns in the sequence and highlights the matching region. (nih.gov)
  • were able to get the machine to specifically target and sequence flu virus RNA. (cdc.gov)
  • Rambo-Martin's work translated the data into something that made sense, and he was able to confirm that the molecular work performed did, in fact, sequence the RNA genomes of the influenza viruses studied. (cdc.gov)
  • The lyophilized, non infectious, encapsidated RNA (Armored RNA) contains the NTD & RBD (nt 1 to 1581 in the spike coding sequence) of the SARS-CoV-2 BavPat1 strain (D614G) and can be used as positive control for extraction and real time RT-PCR. (european-virus-archive.com)
  • Despite the existence of marked sequence conservation between genotypes in the HCV CRE and single-stranded regions, there was no evidence for comparable suppression of variability at either synonymous or non-synonymous sites in the other predicted stem-loop structures. (ox.ac.uk)
  • They did so with the RNA genomes of five influenza (Flu) A viruses, including seasonal influenza A and avian influenza A viruses. (cdc.gov)
  • However, while the genomes of people and other living things consist of DNA, some things that aren't technically "living," such as viruses, have genomes coded by RNA instructions instead. (cdc.gov)
  • As seen with many other bacteria, RNA-seq technology has now become the method of choice for transcriptome analysis in the enterococcus. (frontiersin.org)
  • The Ambion® RNA-Seq Library Construction Kit streamlines high-throughput sequencing of the whole transcriptome and small RNAs, while maintaining strand orientation, on the Illumina® GAII platform. (thermofisher.com)
  • Mammalian transcriptomes contain thousands of long noncoding RNAs (lncRNAs). (biomedcentral.com)
  • Analyses of the mitochondrial hydroxysteroid dehydrogenase (HSD17B10) uncover the RNA-binding specificity of an enigmRBP. (nature.com)
  • Truncation of the human small heterodimer partner (SHP) promoter and deletion analyses revealed VDR-dependent inhibition of SHP, and mobility shift assays showed direct binding of VDR to enhancer regions of SHP. (nih.gov)
  • After 4 weeks of conversion, we performed global analyses of RNA and protein levels by RNA-sequencing and mass spectrometry. (lu.se)
  • Furthermore, the methods used in this study could be used to learn more about other RNA viruses. (cdc.gov)
  • Influenza viruses are an example of an RNA virus. (cdc.gov)
  • Thus, the binding of G3BPs to nsP2 can support CHIKV RNA replication and restore the infectivity of viruses lacking G3BP-binding motifs in the HVD of nsP3. (bvsalud.org)
  • Coronaviruses are enveloped RNA viruses that cause respiratory illnesses of varying severity from the common cold to fatal pneumonia. (msdmanuals.com)
  • The aim of the present study was to reveal the new molecular mechanism of long non‑coding (lnc)RNA XIST in the development of hepatic carcinoma. (spandidos-publications.com)
  • Further, Zamani et al ( 9 ) investigated the epigenetic effects of solute carrier family 25 member 19 in hepatic carcinoma and confirmed that DNA methylation in the functional region of maternally expressed 3 (MEG3) was associated with its loss of expression in hepatic carcinoma. (spandidos-publications.com)
  • Hel-N1, a human RNA-binding protein, shares significant homology with Drosophila protein ELAV, which is essential for fly neuronal development. (duke.edu)
  • We are also using high-resolution cryo-electron microscopy to study the structure of exosomes isolated from neuronal cells and characterise their protein and RNA content using high throughput sequencing and proteomics techniques. (edu.au)
  • these interactions are crucial for CHIKV RNA replication . (bvsalud.org)
  • Insertion of native motifs into nsP1 or nsP2 but not into the C terminus of nsP4 activated CHIKV RNA replication in human cells in a G3BP-dependent manner. (bvsalud.org)
  • 7 CHIKV has probably had an unappreciated circulation in the region due to its disease presentation and co-circulation with DENV. (who.int)
  • To identify a nuclear marker pathognomonic of astrocytic phenotype, we assessed differential RNA expression by FACS-purified adult astrocytes and, on that basis, evaluated the expression of the transcription factor SOX9 in both mouse and human brain. (jneurosci.org)
  • Recently developed unbiased high content techniques to identify RBPs in vivo yielded information on differences in cell type-specific expression and/or RNA-binding activity of RBPs in mammalian cells 2 , 3 . (nature.com)
  • These novel phenotypes imply an important function of the bridge helix and switch regions as an anti-backtracking ratchet and an RNA hydrolysis regulator. (houstonmethodist.org)
  • By modifying the adapter that targets this region, Keller et al. (cdc.gov)
  • That AsiA induces, rather than merely stabilizes, this rearrangement can be realized by comparison to the homologous structures of region 4 solved in a variety of contexts, including the structure of Thermotoga maritima sigmaA region 4 described herein. (rcsb.org)
  • 5'-untranslated region (5'UTR), the hypervariable region 1 (HVR1), non-structural gene 5a (NS5a) and non-structural gene 5b (NS5b). (cdc.gov)
  • Because neutropenic episodes, even with bowel in- Filovirus RNA in Fruit Bats, volvement, are common during treatment for cancer ( 8 ), no reason to promote therapeutic use of probiotics has China been proven. (cdc.gov)
  • In this application note, we demonstrate a simultaneous high-quality DNA and RNA extraction method that does not require splitting the sample lysate. (beckman.com)
  • More recently, another group of researchers reported that they had developed a process for optimizing low- abundance RNA, by combining aRNA amplification with template- switching. (genomicglossaries.com)
  • Un test immuno-enzymatique et une amplification en chaîne par polymérase ont été réalisés. (who.int)
  • PABPN1 alters a region at the end of mRNA molecules that protects mRNA from being broken down. (medlineplus.gov)
  • Because alternative RNA splicing allows different types of mRNA molecules to be created from a single gene, it generates the diversity of protein function and structure that is essential to complex organisms. (genomicglossaries.com)
  • The analysis showed that SOX9+ astrocytes constitute ∼10-20% of the total cell number in most CNS regions, a smaller fraction of total cell number than previously estimated in the normal adult brain. (jneurosci.org)
  • Recent functional studies have defined one such stem-loop structure in the NS5B region as an essential cis-acting replication element (CRE). (ox.ac.uk)
  • Strikingly, removal of the σ 54 Region I is sufficient to invert the action of DksA (from stimulation to inhibition or vice versa) at two test promoters. (houstonmethodist.org)