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  • motifs
  • 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)
  • 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)
  • synthesis
  • 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)
  • 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)
  • lncRNAs
  • 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)
  • 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)
  • 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)
  • Long noncoding RNAs (lncRNAs) emerged as common players acting on epigenetic or transcriptional regulation in several eukaryotic organisms. (springer.com)
  • Roles
  • Here we review the recent findings, which uncovered the direct roles of UPF1 and other NMD-factors in DNA replication and genome maintenance pathways and suggest functional connections between RNA and DNA metabolism. (epfl.ch)
  • RNA-DNA hybrid structures play important roles in the transmission and processing of biological information ( 1 ). (pubmedcentralcanada.ca)
  • The numerous biological roles of RNA-DNA hybrids have prompted great interest in characterization of the structures and the physical properties of these duplexes. (pubmedcentralcanada.ca)
  • Recently, functional experiments have revealed many novel functional roles of RNA modifications. (wikipedia.org)
  • In 2010, He proposed that RNA modifications could be reversible and may have regulatory roles analogous to well-known reversible DNA and protein modifications. (wikipedia.org)
  • genomes
  • 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)
  • 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)
  • genetic
  • 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)
  • The hybrid between template DNA and messenger RNA is the key intermediate in the expression of genetic information. (pubmedcentralcanada.ca)
  • Pseudouridylation of nonsense codons suppresses translation termination both in vitro and in vivo, suggesting that RNA modification may provide a new way to expand the genetic code. (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)
  • 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)
  • reveals
  • Analysis of m6A in mouse brain RNA reveals that m6A levels are low during embryonic development and increase dramatically by adulthood. (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)
  • 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)
  • stable
  • A low pH also reduces the concentration of free hydroxide, and RNA is stable between pH 5 and 6. (bio.net)
  • That loss is moderate, with average RIN (RNA Integration Numbers) range values of 4.5-6.05, in comparison with values of 6.44-7.22 in samples directly transferred to RNAlater™ (protocol A). Among the house keeping genes tested, the B2M is the most stable. (biomedcentral.com)
  • recognition
  • 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)
  • Together, these strand-specific alterations in stability and molecular flexibility may contribute to the recognition and cleavage of RNA-DNA hybrids by RNase H ( 10 , 11 ). (pubmedcentralcanada.ca)
  • pathways
  • Multiple pathways are involved in the anoxia response of SKIP3 including HuR-regulated RNA stability, NF-kappaB and ATF4. (ox.ac.uk)
  • Intriguingly, the human NMD-kinase SMG1 is also involved in genome stability pathways and the human NMD-factor EST1A/SMG6 is telomerase-associated and has been implicated in telomere maintenance. (epfl.ch)
  • 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)
  • affects
  • To explore systematically how RNA quality affects qRT-PCR assay performance, a set of human placenta RNA samples was generated by two protocols handlings of fresh tissue over a progressive time course of 4 days. (biomedcentral.com)
  • biological
  • 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)
  • evaluate the stability
  • There have been only a few studies conducted by laboratories to evaluate the stability of Ebola's RNA throughout time within gathered samples. (vaccinenewsdaily.com)
  • Researchers at the FDA have developed methods to evaluate the stability of rat whole blood expression obtained from RNA sequencing (RNA-seq) and assess changes in whole blood transcriptome profiles in experiments replicated over time. (rna-seqblog.com)
  • 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)
  • transcripts
  • Connected to this, it is likely that the 5' exonuclease activity of RNase J1 can act directly on the 5' end of native transcripts, once the 5' triphosphate is converted to a 5'-monophosphate by an RNA pyrophosphohydrolase (RppH) activity, similar to the one shown recently by Belasco and colleagues to exist in E. coli [ 8 - 9 ]. (pubmedcentralcanada.ca)
  • human
  • Failure of such mechanisms, in particular misexpression of RNA-BP, has been linked to several human diseases. (frontiersin.org)
  • The fragile nature of RNA and the question of RNases enriched tissues such as placenta prompted us to examine the effects of storage time conditions with regard to RNA integrity and gene expression in non fixed human term placenta. (biomedcentral.com)
  • It can affect the activity, localization as well as stability of RNAs, and has been linked with human diseases. (wikipedia.org)
  • structural
  • This approach could also be used to reveal the structural elements that modulate other aspects of RNA behaviour. (scicombinator.com)
  • This RNA contains structural elements within the 3' and 5' UTR that bring about cap independent translation. (wikipedia.org)
  • modifications
  • Epitranscriptomics describes an aspect of molecular genetics, or a study thereof, that depends on biochemical modifications of RNA. (wikipedia.org)
  • There are more than one hundred documented RNA modifications, which are described in a database maintained by the RNA Institute at the University at Albany. (wikipedia.org)
  • Modifying an RNA molecule requires a significant amount of energy from the cell This high energy cost must mean that the cell deems these modifications to be very important. (wikipedia.org)
  • known
  • In the Bangia intron, the partners have been swapped relative to known group I RNAs that include this contact. (utexas.edu)
  • 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)
  • 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)
  • 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)
  • control
  • Expression was measured in globin-depleted RNA extracted from the whole blood of Sprague-Dawley rats, given either saline (control) or neurotoxic doses of amphetamine (AMPH). (rna-seqblog.com)
  • genome stability
  • The role of the Fanconi anemia pathway in DNA repair and maintenance of genome stability]. (nih.gov)
  • While de novo DNA methylation modifies the information passed on by the parent to the progeny, it enables key epigenetic modifications essential for processes such as cellular differentiation and embryonic development, transcriptional regulation, heterochromatin formation, X-inactivation, imprinting and genome stability. (wikipedia.org)
  • protein
  • Altered axon-Schwann cell interactions in PNS myelin-deficient Trembler mice result in changed axonal transport rates, neurofilament and microtubule-associated protein phosphorylation, neurofilament density, and microtubule stability. (jneurosci.org)
  • A La related protein LARP7 is also found associated with 7SK, presumably in part through its interaction with the 3' end of the RNA. (wikipedia.org)
  • small
  • It was shown in a study using the enterohemorrhagic E. coli that unusually short (between 50 and 60 nucleotide long) small RNAs are expressed by bacteriophages and bacteriophage-derived pathogenicity islands. (wikipedia.org)
  • They modulate the activities of bacterial host small RNAs. (wikipedia.org)
  • base
  • The second aircraft carried out manufacturer's trials from Blackburn's new seaplane base at Brough and later flew to the RNAS base at Great Yarmouth for service trials. (wikipedia.org)
  • Cell
  • We found that MMF appears safe, and its use was associated with a decreased T cell activation as well as a short-term decline in plasma HIV-1 RNA. (biomedcentral.com)
  • It has also been found that DNMT3A-mutated cell lines exhibit transcriptome instability, in that they have much more erroneous RNA splicing as compared to their isogenic[disambiguation needed] wildtype counterparts. (wikipedia.org)
  • left
  • Who are We For ergodic download aging nation the economics and the oxford stability of left it draws impressive to receive database. (logcabinstl.org)
  • Since thymine nucleotides are precursors of DNA (but not RNA), the prefix "deoxy" is often left out, i.e., deoxythymidine is often just called thymidine. (wikipedia.org)
  • mouse
  • Both increased microtubule density and reduced microtubule stability were still observed in transgenic mouse nerves, indicating that signals beyond synaptogenesis and the mere presence of compact myelin are required for normal regulation of the axonal microtubule cytoskeleton. (jneurosci.org)