• Genome
  • It consists of a non-coding 222nt sRNA called RatA (RNA anti-toxin A) and a protein toxin named TxpA (Toxic protein A). RatA was discovered in intergenic regions of the B. subtilis genome, in a 728-nucleotide region between genes yqdB (later renamed TxpA) and yqbM. (wikipedia.org)
  • The combined length of repetitive sequences was 26.5 Mb, which accounted for 6.87% of the genome, indicating that the compactness of T. flavidus genome was approximative with that of T. rubripes genome.A total of 1,253 non-coding RNA genes and 30,285 protein-encoding genes were assigned to the genome.This draft genome provides a valuable resource for understanding and improving both fundamental and applied research with pufferfish in the future. (nih.gov)
  • The turnip crinkle virus (TCV) core promoter hairpin (Pr) is an RNA element located in the 3' UTR of the viral genome that is required for minus strand RNA synthesis. (wikipedia.org)
  • In order to insert itself into the genome, retrotransposon encoded protein (R2) protein makes a specific nick in one of the DNA strands at the insertion site and uses the 3′ hydroxyl group exposed by this nick to prime the reverse transcription process termed target primed reverse transcription (TPRT), where the RNA genome is transcribed into DNA. (wikipedia.org)
  • The R2 element 3' UTR RNA is a cis-acting element identified in R2 retrotransposons which is involved in priming the reverse transcription process (an essential part of retrotransposon insertion into the host genome). (wikipedia.org)
  • Flaviviruses have a (+) sense RNA genome and replicate in the cytoplasm of the host cells. (wikipedia.org)
  • regulatory
  • We want to define a dynamic RNA regulatory network for germline development by determining structures of 3'UTRs in vivo and how they change during development. (albany.edu)
  • Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs. (nih.gov)
  • It is a dual-function RNA which acts both as a protein-coding RNA and as a regulatory sRNA. (wikipedia.org)
  • Almost a hundred of small regulatory RNAs have been discovered in E.coli and more than one thousand have been predicted by various computational approaches. (jbsdonline.com)
  • Most known regulatory RNAs are encoded by independent genes (sRNAs), while 15 transcripts are partly generated from the antisense strands of coding sequences (aRNAs) and may affect translation or stability of overlapping mRNAs. (jbsdonline.com)
  • Since strategies used to discover regulatory RNAs were focused primarily on intergenic regions, most aRNAs were found by chance. (jbsdonline.com)
  • The Atlas of UTR Regulatory Activity (AURA), now at its second version, is a manually curated and comprehensive catalog of human 5' and 3' untranslated sequences (UTR) and UTR regulatory annotations. (wikipedia.org)
  • This, along with its presence in the majority of modern phyla, indicates that RNA editing is an essential regulatory gene for metazoan organisms. (wikipedia.org)
  • antisense
  • There is evidence that DsrA RNA can self-assemble into nanostructures through antisense interactions of three self-complementary regions. (wikipedia.org)
  • The highest percentage of promoters followed by putative ORFs (56%) has been found in group I regions, while the smallest one in group A (26%), assuming that most RNAs potentially produced in antisense direction within coding regions may function as untranslated RNAs. (jbsdonline.com)
  • nucleotide
  • These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. (wikipedia.org)
  • transcript
  • Initially, Affymetrix microarrays were used to detect transcription in this region, Northern blot experiments and mutation analysis were then employed to characterise the RNA transcript. (wikipedia.org)
  • The MicX RNA gene overlaps with VCA0943 - a gene coding for a maltose transporter permease - but the ribonuclease RNAase E processes the MicX transcript to create an active and stable form containing only the VCA0943 3' UTR. (wikipedia.org)
  • X-chromosome inactivation (XCI) in female mammals depends on the noncoding RNA X inactivation specific transcript (Xist). (biomedsearch.com)
  • The major 5′ splice site (5′ss) that is positioned in the untranslated leader of the HIV-1 RNA transcript is of particular interest because it is used for the production of the more than 40 differentially spliced subgenomic mRNAs. (mdpi.com)
  • hairpin
  • We previously presented evidence that the major 5′ss is regulated by a repressive local RNA structure, the splice donor (SD) hairpin, that masks the 11 nucleotides (nts) of the 5′ss signal for recognition by U1 small nuclear RNA (snRNA) of the spliceosome machinery. (mdpi.com)
  • A strikingly different multiple-hairpin RNA conformation was recently proposed for this part of the HIV-1 leader RNA. (mdpi.com)
  • The TCV hairpin 5 (H5) is an RNA element found in the turnip crinkle virus. (wikipedia.org)
  • Xist RNA
  • The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization. (biomedsearch.com)
  • While it is established that the 5' region of Xist RNA, comprising the A-repeats and holding 7.5-8.5 copies of a conserved 26-mer sequence, is essential for Xist-mediated silencing, high-resolution structural information for the A-repeats is not available. (biomedsearch.com)
  • This chapter focuses on events downstream from the spread of XIST RNA across the interphase chromosome, to consider how this large noncoding RNA interacts with and silences a whole chromosome. (umassmed.edu)
  • For example, evidence indicates that XIST RNA acts at the architectural level of the whole chromosome to induce formation of a silent core enriched for nongenic and repetitive (Cot-1) DNA, which corresponds to the DAPI-dense Barr body. (umassmed.edu)
  • mRNAs
  • Physico-chemical properties of predicted RNA-products were compared with those of known sRNAs and mRNAs of comparable size. (jbsdonline.com)
  • Humans
  • A) Patterns of the full-length sequence conservation of 826 human ESC-specific NANOG-binding sites (left panel) and 130 genomic loci encoding 33 nt LTR7 RNA (right panel) in genomes of five Modern Humans and three Neanderthals. (nih.gov)
  • So far vault RNAs have been isolated from humans, rodents and bullfrogs. (wikipedia.org)
  • Double-stranded RNA-specific adenosine deaminase is an enzyme that in humans is encoded by the ADAR gene (which stands for adenosine deaminase acting on RNA). (wikipedia.org)
  • gene
  • The gene underlying the disorder, fragile X mental retardation 1 (FMR1), is silenced in most cases by a CGG-repeat expansion mutation in the 5' untranslated region (UTR). (nih.gov)
  • The RyhB gene name is an acronym composed of R for RNA, y for unknown function (after the protein naming convention), with the h representing the ten-minute-interval section of the E. coli map the gene is found in. (wikipedia.org)
  • Early research in the 1990s looked into the specifics of vault RNA and focused around the conservation of the gene in animals. (wikipedia.org)
  • Transcription of the GcvB RNA is activated by the adjacent GcvA gene and repressed by the GcvR gene. (wikipedia.org)
  • Through its intuitive web interface, it furthermore provides full access to a wealth of information that integrates RNA sequence and structure data, variation sites, gene synteny, gene and protein expression and gene functional descriptions from scientific literature and specialized databases. (wikipedia.org)
  • Adenosine Deaminase Acting on RNA (ADAR) and its gene were first discovered accidentally in 1987 as a result of research by Brenda Bass and Harold Weintraub. (wikipedia.org)
  • This likely occurred in the lineage which leads to the crown Metazoa when a duplicate ADAT gene was coupled to a gene encoding at least one double stranded RNA binding. (wikipedia.org)
  • microRNAs
  • Projects in our lab examine the interactions and mechanisms by which RNA viruses such as hepatitis C virus exploit host microRNAs and RNA granules to promote infection. (albany.edu)
  • inactivation
  • Expression of repeat RNAs may contribute to chromosome remodeling, and evidence suggests that other types of repeat elements may be involved in escape from X inactivation. (umassmed.edu)
  • structures
  • We also show that RNA secondary structures can be compared very rapidly by a simple string Edit-Distance algorithm with a minimal loss of accuracy.These datasets allowed for comparison of the algorithm with other methods.In these tests, RNAspa performed better than four other programs. (nih.gov)
  • We also show that RNA secondary structures can be compared very rapidly by a simple string Edit-Distance algorithm with a minimal loss of accuracy. (nih.gov)
  • Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints. (wikipedia.org)
  • Cellular RNA cap structures are formed via the action of an RNA triphosphatase, with guanylyltransferase, N7-methyltransferase and 2′-O methyltransferase. (wikipedia.org)
  • The N-terminal domain of the non-structural protein 5 (NS5) has both the N7-methyltransferase and guanylyltransferase activities necessary for forming mature RNA cap structures. (wikipedia.org)
  • single stranded
  • ADAR2 and ADAR3 have an arginine rich single stranded RNA (ssRNA) binding domain. (wikipedia.org)
  • Flaviviruses share several common aspects: common size (40-65 nm), symmetry (enveloped, icosahedral nucleocapsid), nucleic acid (positive-sense, single-stranded RNA around 10,000-11,000 bases), and appearance in the electron microscope. (wikipedia.org)
  • vivo
  • First, RNA synthesized in vitro competes with the hybridization of [(32)P]rRNA synthesized in vivo to the heavy strand of B. subtilis DNA. (jove.com)
  • Second, unlabeled rRNA synthesized in vivo competes with the hybridization of [(3)H]RNA synthesized in vitro to denatured DNA or heavy-strand DNA, but not to light-strand DNA. (jove.com)
  • small
  • Through recent discoveries, it has been shown that the vault non-coding RNAs produce small vault RNAs through a DICER mechanism. (wikipedia.org)
  • regions
  • Most editing site are found in noncoding regions of RNA such as untranslated regions (UTRs), Alu elements and long interspersed nuclear element (LINEs). (wikipedia.org)
  • Sequence comparisons show evidence for compensatory mutations within the helical regions indicating the secondary structure of the RNA is of biological importance. (wikipedia.org)
  • expression
  • RNA splicing is a critical step in the human immunodeficiency virus type 1 (HIV-1) replication cycle because it controls the expression of the complex viral proteome. (mdpi.com)
  • genomic
  • The genomic RNA is modified at the 5′ end of positive-strand genomic RNA with a cap-1 structure (me7-GpppA-me2). (wikipedia.org)
  • Flavivirus genomic RNA replication occurs on rough endoplasmic reticulum membranes in membranous compartments. (wikipedia.org)
  • molecule
  • A single example of Type III toxin-antitoxin system has been described whereby a protein toxin is bound directly by an RNA molecule. (wikipedia.org)
  • indicates
  • This positioning of the RNA indicates that they could interact with both the interior and exterior of the vault particle. (wikipedia.org)
  • Chemical
  • classify promoters in respect to their coding potential and analyze physico-chemical features of expected RNA-products. (jbsdonline.com)
  • Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function. (wikipedia.org)
  • region
  • A 3' untranslated region variant in FMR1 eliminates neuronal activity-dependent translation of FMRP by disrupting binding of the RNA-binding protei. (nih.gov)
  • The vimentin 3' UTR protein-binding region is an RNA element that contains a Y shaped structure which has been shown to have protein binding activity. (wikipedia.org)
  • An RNA fragment found in the R2 3' untranslated region (3'UTR), has been shown to interact with one copy of R2 protein during TPRT. (wikipedia.org)
  • RyhB
  • Northern blot with RyhB probe on total RNA was performed at an OD600 of 0.5 along with β-galactosidase assays. (nih.gov)
  • function
  • One research project relates to intron dispersal under cell stress, and to the structure and function of a catalytic RNA that is related to mammalian introns and retrotransposons. (albany.edu)
  • Ongoing studies are also addressing the role of long, intergenic non-coding RNAs in regulating stem cell function. (stanford.edu)
  • Post Doctoral Associate: the anti-apoptotic function of virally expressed untranslated RNA. (ucl.ac.uk)
  • occurs
  • This processing occurs via a self-cleaving ribozyme that forms at the 5' junction of the R2 RNA. (wikipedia.org)
  • To date, conservation of structure has only been described in five moth species: Bombyx mori (R2Bm), Samia cynthia (R2Sc), Coscinocera hercules (R2Ch), Callosamia promethea (R2Cpr), Saturnia pyri (R2Spy) Within this 5' protein binding site an RNA pseudoknot structure occurs. (wikipedia.org)