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  • 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)
  • 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)
  • Csx1 contains RNA recognition motifs that are typically found in regulators of RNA processing. (sciencemag.org)
  • gene
  • 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)
  • Evaluation of RNA quality is essential for gene expression analysis, as the presence of degraded samples may influence the interpretation of expression levels. (biomedcentral.com)
  • 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)
  • Growing evidence demonstrates the importance of regulating mRNA localization, stability and translation, in the control of gene expression, both in development and in differentiated cells. (nih.gov)
  • As he explains, "eight is the minimum length required to achieve a topological lock, but more than that would interfere with release of the RNA at the proper time, the end of a gene. (phys.org)
  • Thus, the stability of RNA-seq whole blood transcriptome can be verified by assessing ribosomal protein subunits and immune-related gene expression. (rna-seqblog.com)
  • 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)
  • M.A. Rodriguez-Gabriel, G. Burns, W. H. McDonald, V. Martin, J. R. Yates III, J. Bahler, P. Russell, RNA-binding protein Csx1 mediates global control of gene expression in response to oxidative stress. (sciencemag.org)
  • metabolism
  • 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)
  • polymerase
  • Human RNA polymerase II recognizes a strong transcriptional pause signal in the initially transcribed region of HIV-1. (nih.gov)
  • Our results suggest that the primary determinant of transcriptional pausing is a relatively weak RNA:DNA hybrid that triggers backtracking of RNA polymerase II along the RNA and DNA chains and displaces the RNA 3' OH from the active site. (nih.gov)
  • In contrast, two alternative RNA secondary structures, TAR and anti-TAR, are not required for pausing and affect it only indirectly, rather than through direct interaction with RNA polymerase II. (nih.gov)
  • The behavior of RNA polymerase II at a mutant pause signal supports a two-step, non-equilibrium mechanism in which the rate-determining step is a conformational change in the enzyme, rather than the changes in nucleic-acid base-pairing that accompany backtracking. (nih.gov)
  • 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)
  • 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)
  • nucleus
  • We discuss possible mechanisms through which mRNA, leaving from the nucleus as an RNA-protein complex, might reach its final intracellular destinations and how its access to the translational apparatus might be regulated in time and space. (nih.gov)
  • Recent exciting developments in the field of RNA transport include the revelation that RNA processing, exit from the nucleus and identification in the cytoplasm are related processes, mediated by highly dynamic protein-RNA interactions. (keystonesymposia.org)
  • assay
  • Although its role in either complex has not yet been defined, TEP1 has been shown to interact with the mouse telomerase RNA and with several of the human vault RNAs in a yeast three-hybrid assay. (rupress.org)
  • 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)
  • Quantitative plasma culture and p24 antigen concentrations were determined, and HIV RNA levels in plasma were measured by both reverse transcription-PCR-enzyme-linked immunosorbent assay (RT-PCR-ELISA) and branched DNA methods. (asm.org)
  • The branched DNA probe assay detected a significant decline in HIV RNA equivalent in plasma over 72 h in both collection tubes, the decline being more dramatic in the standard VACUTAINER tube than the CPT tube. (asm.org)
  • lncRNAs
  • 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)
  • 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)
  • structures
  • We analyze the solution condition dependence of the intermediate structures and molecular flux through them on the Mg 2+ -mediated folding of the L-21 Tetrahymena thermophila group I intron and a mutant of reduced stability by varying the background monovalent cation type and concentration. (pnas.org)
  • 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)
  • 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)
  • 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)
  • telomerase
  • Here we show that the levels of the telomerase RNA and its association with the telomerase RNP are also unaffected in mTep1 − / − mice. (rupress.org)
  • Most eukaryotic chromosome ends are maintained by telomerase, a multisubunit RNP complex that uses an RNA template to specify the addition of telomeric DNA onto the chromosome ends (for review see Greider 1996 ). (rupress.org)
  • Here we show that biochemical fractionation of the telomerase complexes and the level of telomerase RNA in cell extracts showed no detectable alterations in mTep1 -deficient mice. (rupress.org)
  • 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)
  • A long-standing obstacle is the contribution of local RNA secondary structure to the definition of interaction partners in a variety of regulatory contexts, including-but not limited to-transcript stability, alternative splicing and localization. (scicombinator.com)
  • duplexes
  • The native-state topology of structured RNA consisting of Watson-Crick duplexes connected by semiflexible junctions and specific long-range tertiary contacts constrains the biopolymer's conformational degrees of freedom ( 21 - 23 ). (pnas.org)
  • functional
  • A fully functional elongation complex contains both an eight-base-pair bubble and an 8-base-pair DNA-RNA duplex. (phys.org)
  • Based on these results, a correlation between RNA length and the functional impact of HAX1 on PBDE expression was supposed. (springer.com)
  • Processing
  • The purpose of this RFA is to stimulate research towards (1) understanding uptake and processing of RNAi by target tissues, (2) assessing stability, half-life and off-target effects in target tissues, and (3) determining optimal delivery methods for uptake by the target tissues. (nih.gov)
  • The loss of the RNA integrity was higher in the placental tissues that underwent a dissection before RNA processing by comparison with those transferred directly into RNA later™ solution. (biomedcentral.com)
  • The quality of qRT-PCR data analysis is strongly related to the integrity and stability of the mRNA extracted from the tissue which is in turn dependent on tissue sample processing. (biomedcentral.com)
  • post-transcriptional
  • Decoding post-transcriptional regulatory programs in RNA is a critical step towards the larger goal of developing predictive dynamical models of cellular behaviour. (scicombinator.com)
  • 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)
  • Quantitative
  • Molecular tools for tissue profiling, such as real-time quantitative RT-PCR, generally require collection of fresh frozen tissues as sources of high-quality RNA. (biomedcentral.com)
  • Stabilities of quantitative plasma culture for human immunodeficiency virus, RNA, and p24 antigen from samples collected in VACUTAINER CPT and standard VACUTAINER tubes. (asm.org)
  • interactions
  • We also focus on a few known examples of aberrant RNA-protein interactions associated with human diseases, including cancer. (nih.gov)
  • But I think it is a reminder that we need to be thinking in three dimensions when modeling RNA-DNA interactions. (phys.org)
  • Biology
  • 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)
  • 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)
  • The work presented in this paper addresses the question of the stability and dynamics of individual base pairs in RNA-DNA hybrids of mixed, but homologous, base sequences. (pubmedcentralcanada.ca)
  • Factors
  • Among the known factors are intermediate stability, electrostatic environment, native-state topology, and the initial conformational ensemble ( 15 ). (pnas.org)