• regulation
  • Discovery of new ribonuclease activities in B. subtilis and other Gram-positive species, especially the dual-functioning RNase J1, which specifies both an endonuclease activity and the long-sought bacterial 5'-to-3' exoribonuclease activity, has led to the recognition of intriguing mechanisms of gene regulation at the level of RNA decay. (pubmedcentralcanada.ca)
  • Investigation will continue in Martin's laboratory on transcription in general and on the role of RNA polymerase in the proper regulation of RNA synthesis, including the starting or promoter sequences and termination message that ends it. (phys.org)
  • These m6A readers, together with m6A methyltransferases (writers) and demethylases (erasers), establish a complex mechanism of m6A regulation in which writers and erasers determine the distributions of m6A on RNA, whereas readers mediate m6A-dependent functions. (wikipedia.org)
  • This non-coding RNA was identified in Neisseria meningitidis and is involved in iron regulation of the succinate dehydrogenase genes sdhA and sdhC. (wikipedia.org)
  • motifs
  • Modulation of messenger RNA stability is usually mediated by stabilizing or destabilizing RNA-binding proteins (RNA-BP) that bind to the 3′-untranslated region regulatory motifs, such as AU-rich elements (AREs). (frontiersin.org)
  • A fundamental property of RNA is that its secondary structure and even some tertiary contacts are highly stable, which gives rise to independent modular RNA motifs and makes RNAs prone to adopting misfolded intermediates. (utexas.edu)
  • This result underscores the modular nature of RNA motifs and provides insight into how structured RNAs can arrange helices and contacts in multiple ways to achieve and stabilize functional structures. (utexas.edu)
  • Here we present a computational framework based on context-free grammars and mutual information that systematically explores the immense space of small structural elements and reveals motifs that are significantly informative of genome-wide measurements of RNA behaviour. (scicombinator.com)
  • AUF1, also known as hnRNP D, binds AREs through RNA recognition motifs (RRMs). (wikipedia.org)
  • synthesis
  • Hybrid structures between RNA and DNA strands serve as initiation sites for the synthesis of Okazaki fragments in DNA replication and as sites for the elongation of telomeric repeats by telomerase. (pubmedcentralcanada.ca)
  • This structure and several downstream stem-loops are required for synthesis of the negative strand RNA. (wikipedia.org)
  • mRNAs
  • Although the transcriptional mechanisms that regulate the production of specific mRNAs are undoubtedly important, it has become increasingly evident that processes regulating the stability of mRNAs also represent critical steps in the control of dynamic gene expression. (frontiersin.org)
  • Utilizing a custom noncoding RNA array, we determined the half-lives of ∼800 lncRNAs and ∼12,000 mRNAs in the mouse Neuro-2a cell line. (ox.ac.uk)
  • AREs) are found in the 3' untranslated region (UTR) of many messenger RNAs (mRNAs) that code for proto-oncogenes, nuclear transcription factors, and cytokines. (wikipedia.org)
  • polymerase
  • PhysOrg.com) -- A pair of University of Massachusetts Amherst chemists believe they have for the first time explained how the main players in transcription -- RNA polymerase, RNA (red in illustration) and the DNA template (blue) -- come together and link tightly enough to create a stable complex while DNA unwinds to pass crucial genetic information to RNA, but not so tightly that they can't come apart easily once transcription is complete. (phys.org)
  • In it, a flexible thread of RNA winds around the ladder-like DNA strand , creating a loop that locks them together as RNA polymerase makes RNA from the DNA template. (phys.org)
  • However, with this new understanding of the topological lock, in which RNA polymerase loops around and through the DNA template, it seems more clear why eight base pairs is optimal, Martin notes. (phys.org)
  • 1. Would a primer extension reaction in DNA sequencing work using an RNA polymerase? (biology-online.org)
  • genomes
  • Transcriptomic analyses have identified tens of thousands of intergenic, intronic, and cis-antisense long noncoding RNAs (lncRNAs) that are expressed from mammalian genomes. (ox.ac.uk)
  • The complementarities between bases in the RNA-DNA hybridization reaction is also the basis for a variety of applications, such as identification of specific of sites genomes by in situ hybridization, the antisense technology, and microarray gene expression profiling. (pubmedcentralcanada.ca)
  • The presence of tRNA-like structures has been demonstrated in many plant virus RNA genomes. (wikipedia.org)
  • intergenic
  • Analysis of lncRNA features revealed that intergenic and cis-antisense RNAs are more stable than those derived from introns, as are spliced lncRNAs compared to unspliced (single exon) transcripts. (ox.ac.uk)
  • novel
  • To explore further how RNAs gain stability from intricate architectures, we examined a novel group I intron from red algae (Bangia). (utexas.edu)
  • A novel database, RMBase (http://mirlab.sysu.edu.cn/rmbase/), has provide various web interfaces to show all RNA modification sites identified from above-mentioned sequencing technologies. (wikipedia.org)
  • vitro
  • In this work, we found that a version of the intron that was generated by in vitro selection for enhanced stability also displayed enhanced specificity against a stable misfolded structure that is globally similar to the native state, despite the absence of selective pressure to increase the energy gap between these structures. (utexas.edu)
  • In vitro, this methyltransferase complex preferentially methylates RNA oligonucleotides containing GGACU and a similar preference was identified in vivo in mapped m6A sites in Rous sarcoma virus genomic RNA and in bovine prolactin mRNA. (wikipedia.org)
  • tRNA
  • The known purposes for this kind of modification is to allow for a bigger difference between the tRNA molecules so that tRNAMet is distinguished from elongator tRNAMet and tRNA stability. (wikipedia.org)
  • decay
  • In this article, we focus on regulated RNA decay in the control of gene expression in Gram-positive organisms, with a focus on Bacillus subtilis . (pubmedcentralcanada.ca)
  • In this review, we discuss examples of regulated RNA decay in Gram-positive bacteria that are necessary for proper gene function. (pubmedcentralcanada.ca)
  • The RNA genome of RSV contains an extremely long 3' UTR that ranges between 5-7 kb in length which would usually direct it toward nonsense mediated decay (NMD) within the eukaryotic host cell. (wikipedia.org)
  • nuclear
  • Nuclear magnetic resonance spectroscopy and proton exchange have been used to characterize two RNA-DNA hybrids from the tR2 intrinsic transcription terminator site of phage λ. (pubmedcentralcanada.ca)
  • regulatory
  • Despite recent efforts, the vast landscape of RNA regulatory elements remains largely uncharacterized. (scicombinator.com)
  • There are many documented instances where the presence of a structural regulatory element dictates alternative splicing patterns (for example, human cardiac troponin T) or affects other aspects of RNA biology. (scicombinator.com)
  • transcript
  • They found that splicing is inhibited if uridines in RNA transcript were replaced by BrU, which suggested that Us were critical for the splicing reaction. (wikipedia.org)
  • The RNA chaperone Hfq acts to enhance binding of NrrF or stabilizes the NrrF/sdh transcript duplex. (wikipedia.org)
  • Translation
  • Although the gene for this RNA contains open reading frames, translation studies found no protein product hence gadd7 has been classified as non-coding RNA. (wikipedia.org)
  • This RNA contains structural elements within the 3' and 5' UTR that bring about cap independent translation. (wikipedia.org)
  • cDNA
  • In practice, people who are very concerned about the quality of, say, an mRNA prep to be used as a source for cDNA or mapping, will store the RNA as an ethanol precipitate. (bio.net)
  • As with all retroviruses, it reverse transcribes its RNA genome into cDNA before integration into the host DNA. (wikipedia.org)
  • Modulation
  • Additionally, silencing the m6A methyltransferase significantly affects gene expression and alternative RNA splicing patterns, resulting in modulation of the p53 (also known as TP53) signalling pathway and apoptosis. (wikipedia.org)
  • genes
  • NrrF acts as an antisense RNA and is complementary to the junction between the second and third genes of the sdh operon (sdhD and sdhA). (wikipedia.org)
  • strands
  • The hybrids have the same base sequence: 5'-GGCGCAGGCC(T/U)(T/U)CC-3'/5'-GGAAGGCC(T/U)GCGCC-3', but differ from each other by an interchange of DNA and RNA strands. (pubmedcentralcanada.ca)
  • This property has been first demonstrated for RNA-DNA hybrid duplexes with polypurine and polypyrimidine strands: the hybrid with a polypurine DNA strand is significantly less stable than the hybrid with a polypurine RNA strand ( 15 - 17 ). (pubmedcentralcanada.ca)
  • RCNMV contains a genome that encodes for two positive sense RNA strands known as RNA1 and RNA2 and both these RNA strands lack a 5' cap and a 3' poly (A) tail. (wikipedia.org)
  • lncRNAs
  • Surprisingly, one of the least stable lncRNAs is the well-characterized paraspeckle RNA Neat1, suggesting Neat1 instability contributes to the dynamic nature of this subnuclear domain. (ox.ac.uk)
  • modification
  • RNA modification occurs in all living organisms, and is one of the most evolutionarily conserved properties of RNAs. (wikipedia.org)
  • Once these questions are answered and biologists have a better sense of the amount of variation in RNA modification, the focus will turn to each modification's biological function. (wikipedia.org)
  • eukaryotes
  • Vaults from higher eukaryotes also contain one or several small vault RNAs (vRNAs, also known as vtRNAs) of 86-141 bases within. (wikipedia.org)
  • stable
  • A low pH also reduces the concentration of free hydroxide, and RNA is stable between pH 5 and 6. (bio.net)
  • termination
  • The two hybrids investigated correspond to RNA-DNA hybrids formed during transcription at the intrinsic transcription termination site tR2 of phage λ ( 18 ). (pubmedcentralcanada.ca)
  • structures
  • These results provide the first demonstration that, for RNA-DNA hybrid structures with the same base sequence, the opening dynamics and the stability of individual base pairs is strongly influenced by the chemical nature of each strand. (pubmedcentralcanada.ca)
  • Thermodynamic analyses have revealed that the stability of hybrid structures is strongly influenced by the base sequence ( 12 - 14 ). (pubmedcentralcanada.ca)
  • Many functional RNAs are required to fold into specific three-dimensional structures. (utexas.edu)
  • Consequently, in addition to stabilizing the native structure relative to the unfolded species (defined here as stability), RNAs are faced with the challenge of stabilizing the native structure relative to alternative structures (defined as structural specificity). (utexas.edu)
  • Our results suggest that the structural rigidity and intricate networks of contacts inherent to structured RNAs can allow them to evolve exquisite structural specificity without explicit negative selection, even against closely-related alternative structures. (utexas.edu)
  • The secondary structures within the 5'UTR was shown to also play a role in RNA stability. (wikipedia.org)
  • reveals
  • Analysis of m6A in mouse brain RNA reveals that m6A levels are low during embryonic development and increase dramatically by adulthood. (wikipedia.org)
  • introns
  • Self-splicing group I introns have been used to study RNA structure and folding for decades. (utexas.edu)
  • base pairs
  • Why an eight base pair duplex is usually involved, and not four or 12, has usually been explained, he adds, by assuming that eight is the minimum number of base pairs able to confer the required stability, but this has never been fully explored. (phys.org)
  • The opening of single base pairs in the two hybrids is characterized by measuring the rates of exchange of imino protons with solvent protons as a function of the concentration of a proton acceptor (ammonia base) at 10 °C. The free energy change in the opening reaction provides a measure of the stability of the base pair, while the rates of opening and closing define the base-pair dynamics. (pubmedcentralcanada.ca)
  • The differences in stability are enhanced when two dA-rU base pairs are located next to each other in the hybrid structure. (pubmedcentralcanada.ca)
  • For the G-C base pairs, the rates of opening and closing, and the stability are affected by the base sequence context and by the nature of the sugar moiety attached to the guanine. (pubmedcentralcanada.ca)
  • Two G-C base pairs (namely, those in the 4th and 10th positions) exhibit large differences in their opening and closing rates between the two hybrids, while maintaining the same stability. (pubmedcentralcanada.ca)
  • known
  • In the Bangia intron, the partners have been swapped relative to known group I RNAs that include this contact. (utexas.edu)
  • interaction
  • Specifically, they say the old one-dimensional "train track" model of the DNA-RNA interaction can now be replaced with a more elegant one. (phys.org)
  • duplex
  • A fully functional elongation complex contains both an eight-base-pair bubble and an 8-base-pair DNA-RNA duplex. (phys.org)