rna

Summary

Summary: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)

Top Publications

  1. Cerase A, Smeets D, Tang Y, Gdula M, Kraus F, Spivakov M, et al. Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy. Proc Natl Acad Sci U S A. 2014;111:2235-40 pubmed publisher
    ..directed recruitment of chromatin modifying factors by the master regulator, X-inactive specific transcript (Xist) RNA, which localizes in cis along the entire length of the chromosome...
  2. Tumbale P, Williams J, Schellenberg M, Kunkel T, Williams R. Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity. Nature. 2014;506:111-5 pubmed publisher
    ..APTX efficiently repairs adenylated RNA-DNA, and acting in an RNA-DNA damage response (RDDR), promotes cellular survival and prevents S-phase checkpoint ..
  3. Tessarz P, Santos Rosa H, Robson S, Sylvestersen K, Nelson C, Nielsen M, et al. Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification. Nature. 2014;505:564-8 pubmed publisher
    ..Together these data identify glutamine methylation of H2A as the first histone epigenetic mark dedicated to a specific RNA polymerase and define its function as a regulator of FACT interaction with nucleosomes.
  4. Hui L, Wick H, Edlow A, Cowan J, Bianchi D. Global gene expression analysis of term amniotic fluid cell-free fetal RNA. Obstet Gynecol. 2013;121:1248-54 pubmed publisher
    To identify the tissue expression patterns and biological pathways enriched in term amniotic fluid cell-free fetal RNA by comparing functional genomic analyses of term and second-trimester amniotic fluid supernatants...
  5. Donnelly C, Zhang P, Pham J, Haeusler A, Heusler A, Mistry N, et al. RNA toxicity from the ALS/FTD C9ORF72 expansion is mitigated by antisense intervention. Neuron. 2013;80:415-28 pubmed publisher
    ..cell (iPSC)-differentiated neurons from C9ORF72 ALS patients revealed disease-specific (1) intranuclear GGGGCCexp RNA foci, (2) dysregulated gene expression, (3) sequestration of GGGGCCexp RNA binding protein ADARB2, and (4) ..
  6. Salzman J, Chen R, Olsen M, Wang P, Brown P. Cell-type specific features of circular RNA expression. PLoS Genet. 2013;9:e1003777 pubmed publisher
    Thousands of loci in the human and mouse genomes give rise to circular RNA transcripts; at many of these loci, the predominant RNA isoform is a circle...
  7. Garcia Martin J, Clote P, Dotu I. RNAiFOLD: a constraint programming algorithm for RNA inverse folding and molecular design. J Bioinform Comput Biol. 2013;11:1350001 pubmed publisher
    ..In this paper, we present a Constraint Programming (CP) approach to solve the RNA inverse folding problem...
  8. Hussain S, Sajini A, Blanco S, Dietmann S, Lombard P, Sugimoto Y, et al. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep. 2013;4:255-61 pubmed publisher
    ..NSun2 is an RNA methyltransferase modifying cytosine-5 in transfer RNAs (tRNAs), yet the identification of cytosine methylation in ..
  9. Ling S, Polymenidou M, Cleveland D. Converging mechanisms in ALS and FTD: disrupted RNA and protein homeostasis. Neuron. 2013;79:416-38 pubmed publisher
    ..Dysfunction in RNA processing and protein homeostasis is an emerging theme...

More Information

Publications83

  1. Sarkies P, Miska E. RNAi pathways in the recognition of foreign RNA: antiviral responses and host-parasite interactions in nematodes. Biochem Soc Trans. 2013;41:876-80 pubmed publisher
    The nematode Caenorhabditis elegans was the first animal for which RNAi (RNA interference) in response to exogenous triggers was shown experimentally and subsequently the molecular components of the RNAi pathway have been characterized ..
  2. Goldfarb K, Cech T. 3' terminal diversity of MRP RNA and other human noncoding RNAs revealed by deep sequencing. BMC Mol Biol. 2013;14:23 pubmed publisher
    Post-transcriptional 3' end processing is a key component of RNA regulation...
  3. Sookruksawong S, Sun F, Liu Z, Tassanakajon A. RNA-Seq analysis reveals genes associated with resistance to Taura syndrome virus (TSV) in the Pacific white shrimp Litopenaeus vannamei. Dev Comp Immunol. 2013;41:523-33 pubmed publisher
    ..vannamei. High-throughput RNA-Seq was employed, obtaining 193.6 and 171...
  4. Kohlway A, Luo D, Rawling D, Ding S, Pyle A. Defining the functional determinants for RNA surveillance by RIG-I. EMBO Rep. 2013;14:772-9 pubmed publisher
    Retinoic acid-inducible gene-I (RIG-I) is an intracellular RNA sensor that activates the innate immune machinery in response to infection by RNA viruses...
  5. Marchal J, Dal Pan A, Epelbaum J, Blanc S, Mueller S, Wittig Kieffer M, et al. Calorie restriction and resveratrol supplementation prevent age-related DNA and RNA oxidative damage in a non-human primate. Exp Gerontol. 2013;48:992-1000 pubmed publisher
    ..We hypothesized that both CR and RSV impact oxidative DNA and RNA damage compared to standard-fed control (CTL) animals...
  6. Hu L, Chi B, Kuhn M, Filippova E, Walker Peddakotla A, Bäsell K, et al. Acetylation of the response regulator RcsB controls transcription from a small RNA promoter. J Bacteriol. 2013;195:4174-86 pubmed publisher
    ..We propose that acetylation inhibits RcsB activity and that some of this inhibition acts through the acetylation of Lys-154. ..
  7. Datta K, Wolkerstorfer A, Szolar O, Cusack S, Klumpp K. Characterization of PA-N terminal domain of Influenza A polymerase reveals sequence specific RNA cleavage. Nucleic Acids Res. 2013;41:8289-99 pubmed publisher
    ..PA is a sequence selective endonuclease with distinct preference to cleave at the 3' end of a guanine (G) base in RNA. The G specificity is exhibited by the native influenza polymerase complex associated with viral ribonucleoprotein ..
  8. O Neil D, Glowatz H, Schlumpberger M. Ribosomal RNA depletion for efficient use of RNA-seq capacity. Curr Protoc Mol Biol. 2013;Chapter 4:Unit 4.19 pubmed publisher
    Ribosomal RNA (rRNA) is the most highly abundant component of RNA, comprising the majority (>80% to 90%) of the molecules present in a total RNA sample...
  9. Da Costa J, Andreiev A, Dieckmann T. Thermodynamics and kinetics of adaptive binding in the malachite green RNA aptamer. Biochemistry. 2013;52:6575-83 pubmed publisher
    ..the structure of a ligand and thereby incorporating it into their three-dimensional fold, is a key feature of most RNA aptamers...
  10. Nawrocki E, Eddy S. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013;29:2933-5 pubmed publisher
    Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input...
  11. Fernandes A, Macklaim J, Linn T, Reid G, Gloor G. ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq. PLoS ONE. 2013;8:e67019 pubmed publisher
    ..The high per-sample cost of RNA-Seq often precludes the large number of experiments needed to partition observed variance into these categories as ..
  12. Lambert N, Robertson A, Jangi M, McGeary S, Sharp P, Burge C. RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins. Mol Cell. 2014;54:887-900 pubmed publisher
    Specific protein-RNA interactions guide posttranscriptional gene regulation...
  13. Osawa T, Inanaga H, Numata T. Crystal structure of the Cmr2-Cmr3 subcomplex in the CRISPR-Cas RNA silencing effector complex. J Mol Biol. 2013;425:3811-23 pubmed publisher
    ..Cmr proteins (Cmr1-6) and crRNA form a sequence-specific RNA silencing effector complex...
  14. Schwartz J, Wang X, Podell E, Cech T. RNA seeds higher-order assembly of FUS protein. Cell Rep. 2013;5:918-25 pubmed publisher
    The abundant nuclear RNA binding protein FUS binds the C-terminal domain (CTD) of RNA polymerase II in an RNA-dependent manner, affecting Ser2 phosphorylation and transcription...
  15. Lapointe C, Wickens M. The nucleic acid-binding domain and translational repression activity of a Xenopus terminal uridylyl transferase. J Biol Chem. 2013;288:20723-33 pubmed publisher
    ..We also demonstrated that XTUT7 repressed translation of a polyadenylated RNA, to which it added a distinct number of uridines...
  16. Parker D, Xiao Y, Aguilar J, Silverman S. DNA catalysis of a normally disfavored RNA hydrolysis reaction. J Am Chem Soc. 2013;135:8472-5 pubmed publisher
    ..Alternatively, numerous deoxyribozymes have been identified for catalysis of RNA cleavage by 2'-hydroxyl transesterification, forming 2',3'-cyclic phosphate and 5'-hydroxyl termini...
  17. Qian F, Chung L, Zheng W, Bruno V, Alexander R, Wang Z, et al. Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis. Viruses. 2013;5:1664-81 pubmed publisher
    ..Here we used a high-throughput method based on a novel gene expression analysis, RNA-Seq, to give a global picture of differential gene expression by primary human macrophages of 10 healthy donors ..
  18. Guo X, Zhang T, Hu Z, Zhang Y, Shi Z, Wang Q, et al. Efficient RNA/Cas9-mediated genome editing in Xenopus tropicalis. Development. 2014;141:707-14 pubmed publisher
    ..Thus, easy and efficient genome editing tools are still highly desirable for this species. Here, we report that RNA-guided Cas9 nuclease resulted in precise targeted gene disruption in all ten X...
  19. Binzel D, Khisamutdinov E, Guo P. Entropy-driven one-step formation of Phi29 pRNA 3WJ from three RNA fragments. Biochemistry. 2014;53:2221-31 pubmed publisher
    The emerging field of RNA nanotechnology necessitates creation of functional RNA nanoparticles but has been limited by particle instability...
  20. Tran H, Piro B, Reisberg S, Duc H, Pham M. Antibodies directed to RNA/DNA hybrids: an electrochemical immunosensor for microRNAs detection using graphene-composite electrodes. Anal Chem. 2013;85:8469-74 pubmed publisher
    ..The sensor exhibits high selectivity as it distinguishes mismatch. To double-check its selectivity, two specific RNA-DNA antibodies recognizing miRNA-DNA heteroduplexes, antipoly(A)-poly(dT) and anti-S9.6, were used...
  21. Kaforou M, Wright V, Oni T, French N, Anderson S, Bangani N, et al. Detection of tuberculosis in HIV-infected and -uninfected African adults using whole blood RNA expression signatures: a case-control study. PLoS Med. 2013;10:e1001538 pubmed publisher
    ..We hypothesized that a unique host blood RNA transcriptional signature would distinguish TB from other diseases (OD) in HIV-infected and -uninfected patients, ..
  22. Bellaousov S, Reuter J, Seetin M, Mathews D. RNAstructure: Web servers for RNA secondary structure prediction and analysis. Nucleic Acids Res. 2013;41:W471-4 pubmed publisher
    RNAstructure is a software package for RNA secondary structure prediction and analysis. This contribution describes a new set of web servers to provide its functionality...
  23. Chao S, Ying J, Liew G, Marshall W, Liew C, Burakoff R. Blood RNA biomarker panel detects both left- and right-sided colorectal neoplasms: a case-control study. J Exp Clin Cancer Res. 2013;32:44 pubmed publisher
    ..A minimally invasive test that can detect both left-sided and right-sided lesions could increase the effectiveness of screening colonoscopy by revealing the potential presence of neoplasms in the right-sided "blind spot"...
  24. Ramírez Bello J, Vargas Alarcon G, Tovilla Zarate C, Fragoso J. [Single nucleotide polymorphisms (SNPs): functional implications of regulatory-SNP (rSNP) and structural RNA (srSNPs) in complex diseases]. Gac Med Mex. 2013;149:220-8 pubmed
    ..the alternative, mRNA stability and protein function (without altering its structure), they are called structural RNA SNPs (srSNPs). Several studies have identified to these polymorphisms associated with different common diseases e.g...
  25. Sponer J, Sponer J, Mládek A, Banas P, Jurecka P, Otyepka M. How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods. 2013;64:3-11 pubmed publisher
    ..The qualitative difference between QM and molecular mechanics (MM, force field) computations is discussed. We also explain relation of QM and molecular simulation computations to experiments. ..
  26. Dykeman E, Stockley P, Twarock R. Packaging signals in two single-stranded RNA viruses imply a conserved assembly mechanism and geometry of the packaged genome. J Mol Biol. 2013;425:3235-49 pubmed publisher
    The current paradigm for assembly of single-stranded RNA viruses is based on a mechanism involving non-sequence-specific packaging of genomic RNA driven by electrostatic interactions...
  27. Petkovic S, Muller S. RNA self-processing: formation of cyclic species and concatemers from a small engineered RNA. FEBS Lett. 2013;587:2435-40 pubmed publisher
    We have engineered a self-processing RNA, derived from the hairpin ribozyme that runs through a cascade of cleavage and ligation reactions thereby changing its topology...
  28. Kielpinski L, Vinther J. Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res. 2014;42:e70 pubmed publisher
    Hydroxyl Radical Footprinting (HRF) is a tried-and-tested method for analysis of the tertiary structure of RNA and for identification of protein footprints on RNA...
  29. Tatematsu M, Seya T, Matsumoto M. Beyond dsRNA: Toll-like receptor 3 signalling in RNA-induced immune responses. Biochem J. 2014;458:195-201 pubmed publisher
    ..Recently, a TLR3 agonist was identified, which was a virus-derived 'structured' RNA with incomplete stem structures...
  30. Nahvi A, Green R. Structural analysis of RNA backbone using in-line probing. Methods Enzymol. 2013;530:381-97 pubmed publisher
    To determine the secondary structure characteristics of nucleotides in an RNA polymer.
  31. Haas B, Papanicolaou A, Yassour M, Grabherr M, Blood P, Bowden J, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8:1494-512 pubmed publisher
    De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary ..
  32. Lohman G, Zhang Y, Zhelkovsky A, Cantor E, Evans T. Efficient DNA ligation in DNA-RNA hybrid helices by Chlorella virus DNA ligase. Nucleic Acids Res. 2014;42:1831-44 pubmed publisher
    Single-stranded DNA molecules (ssDNA) annealed to an RNA splint are notoriously poor substrates for DNA ligases. Herein we report the unexpectedly efficient ligation of RNA-splinted DNA by Chlorella virus DNA ligase (PBCV-1 DNA ligase)...
  33. Kuhlmann S, Valkov E, Stewart M. Structural basis for the molecular recognition of polyadenosine RNA by Nab2 Zn fingers. Nucleic Acids Res. 2014;42:672-80 pubmed publisher
    The yeast poly(A) RNA binding protein, Nab2, facilitates poly(A) tail length regulation together with targeting transcripts to nuclear pores and their export to the cytoplasm...
  34. Khoddami V, Cairns B. Identification of direct targets and modified bases of RNA cytosine methyltransferases. Nat Biotechnol. 2013;31:458-64 pubmed publisher
    The extent and biological impact of RNA cytosine methylation are poorly understood, in part owing to limitations of current techniques for determining the targets of RNA methyltransferases...
  35. Sternberg S, Redding S, Jinek M, Greene E, Doudna J. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature. 2014;507:62-7 pubmed publisher
    The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria...
  36. Pasek M, Harnmeijer J, Buick R, Gull M, Atlas Z. Evidence for reactive reduced phosphorus species in the early Archean ocean. Proc Natl Acad Sci U S A. 2013;110:10089-94 pubmed publisher
    It has been hypothesized that before the emergence of modern DNA-RNA-protein life, biology evolved from an "RNA world...
  37. Reinharz V, Ponty Y, Waldispühl J. A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution. Bioinformatics. 2013;29:i308-15 pubmed publisher
    The design of RNA sequences folding into predefined secondary structures is a milestone for many synthetic biology and gene therapy studies. Most of the current software uses similar local search strategies (i.e...
  38. Roume H, Heintz Buschart A, Muller E, Wilmes P. Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample. Methods Enzymol. 2013;531:219-36 pubmed publisher
    ..Further, we describe a methodological workflow for the reproducible isolation of concomitant metabolites, RNA (optionally split into large and small RNA fractions), DNA, and proteins...
  39. Attwater J, Wochner A, Holliger P. In-ice evolution of RNA polymerase ribozyme activity. Nat Chem. 2013;5:1011-8 pubmed publisher
    ..In particular, self-replication through RNA-catalysed templated RNA synthesis is thought to have supported a primordial 'RNA world'...
  40. Haas C, Hanson E, Anjos M, Ballantyne K, Banemann R, Bhoelai B, et al. RNA/DNA co-analysis from human menstrual blood and vaginal secretion stains: results of a fourth and fifth collaborative EDNAP exercise. Forensic Sci Int Genet. 2014;8:203-12 pubmed publisher
    The European DNA Profiling Group (EDNAP) organized a fourth and fifth collaborative exercise on RNA/DNA co-analysis for body fluid identification and STR profiling...
  41. Gasiunas G, Siksnys V. RNA-dependent DNA endonuclease Cas9 of the CRISPR system: Holy Grail of genome editing?. Trends Microbiol. 2013;21:562-7 pubmed publisher
    ..Reprogramming of these nucleases to cut genomes at specific locations requires major protein engineering efforts. RNA-guided DNA endonuclease Cas9 of the type II (clustered regularly interspaced short palindromic repeat) CRISPR-Cas ..
  42. Hoshina S, Yura K, Teranishi H, Kiyasu N, Tominaga A, Kadoma H, et al. Human origin recognition complex binds preferentially to G-quadruplex-preferable RNA and single-stranded DNA. J Biol Chem. 2013;288:30161-71 pubmed publisher
    ..Here we report that human ORC binds preferentially to G-quadruplex (G4)-preferable G-rich RNA or single-stranded DNA (ssDNA)...
  43. Sczepanski J, Joyce G. Binding of a structured D-RNA molecule by an L-RNA aptamer. J Am Chem Soc. 2013;135:13290-3 pubmed publisher
    An L-RNA aptamer was developed that binds the natural D-form of the HIV-1 trans-activation responsive (TAR) RNA. The aptamer initially was obtained as a D-aptamer against L-TAR RNA through in vitro selection...
  44. Hou Z, Zhang Y, Propson N, Howden S, Chu L, Sontheimer E, et al. Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc Natl Acad Sci U S A. 2013;110:15644-9 pubmed publisher
    ..Recently, an RNA-guided, DNA-cleaving interference pathway from bacteria [the type II clustered, regularly interspaced, short ..
  45. Chukkapalli V, Inlora J, Todd G, Ono A. Evidence in support of RNA-mediated inhibition of phosphatidylserine-dependent HIV-1 Gag membrane binding in cells. J Virol. 2013;87:7155-9 pubmed publisher
    ..In in vitro systems, matrix-bound RNA suppresses Gag interactions with phosphatidylserine, an acidic lipid prevalent in various cytoplasmic membranes, ..
  46. Shelkovnikova T, Peters O, Deykin A, Connor Robson N, Robinson H, Ustyugov A, et al. Fused in sarcoma (FUS) protein lacking nuclear localization signal (NLS) and major RNA binding motifs triggers proteinopathy and severe motor phenotype in transgenic mice. J Biol Chem. 2013;288:25266-74 pubmed publisher
    ..related proteins, FUS and TAR DNA-binding protein of 43 kDa (TDP-43), implicated in crucial steps of cellular RNA metabolism can cause amyotrophic lateral sclerosis (ALS) and certain other neurodegenerative diseases...
  47. Mansour F, Pestov D. Separation of long RNA by agarose-formaldehyde gel electrophoresis. Anal Biochem. 2013;441:18-20 pubmed publisher
    We describe a method to facilitate electrophoretic separation of high-molecular-weight RNA species, such as ribosomal RNAs and their precursors, on agarose-formaldehyde gels...
  48. Kilburn D, Roh J, Behrouzi R, Briber R, Woodson S. Crowders perturb the entropy of RNA energy landscapes to favor folding. J Am Chem Soc. 2013;135:10055-63 pubmed publisher
    ..We have shown previously that molecular crowding stabilizes folded RNA structures...
  49. Huang J, Voß B. Analysing RNA-kinetics based on folding space abstraction. BMC Bioinformatics. 2014;15:60 pubmed publisher
    b>RNA molecules, especially non-coding RNAs, play vital roles in the cell and their biological functions are mostly determined by structural properties...
  50. Sheng J, Li L, Engelhart A, Gan J, Wang J, Szostak J. Structural insights into the effects of 2'-5' linkages on the RNA duplex. Proc Natl Acad Sci U S A. 2014;111:3050-5 pubmed publisher
    The mixture of 2'-5' and 3'-5' linkages generated during the nonenzymatic replication of RNA has long been regarded as a central problem for the origin of the RNA world...
  51. Dutertre M, Lambert S, Carreira A, Amor Gueret M, Vagner S. DNA damage: RNA-binding proteins protect from near and far. Trends Biochem Sci. 2014;39:141-9 pubmed publisher
    Recent work, including large-scale genetic and molecular analyses, identified RNA-binding proteins (RBPs) as major players in the prevention of genome instability...
  52. Rodríguez Gascón A, del Pozo Rodríguez A, Solinís M. Development of nucleic acid vaccines: use of self-amplifying RNA in lipid nanoparticles. Int J Nanomedicine. 2014;9:1833-43 pubmed publisher
    Self-amplifying RNA or RNA replicon is a form of nucleic acid-based vaccine derived from either positive-strand or negative-strand RNA viruses...
  53. Kladwang W, Mann T, Becka A, Tian S, Kim H, Yoon S, et al. Standardization of RNA chemical mapping experiments. Biochemistry. 2014;53:3063-5 pubmed publisher
    Chemical mapping experiments offer powerful information about RNA structure but currently involve ad hoc assumptions in data processing...
  54. Al Furoukh N, Goffart S, Szibor M, Wanrooij S, Braun T. Binding to G-quadruplex RNA activates the mitochondrial GTPase NOA1. Biochim Biophys Acta. 2013;1833:2933-2942 pubmed publisher
    ..To identify nucleic acids that bind to the RNA-binding domain of NOA1 we employed SELEX (Systemic Evolution of Ligands by EXponential Enrichment) using ..
  55. Varmira K, Hosseinimehr S, Noaparast Z, Abedi S. An improved radiolabelled RNA aptamer molecule for HER2 imaging in cancers. J Drug Target. 2014;22:116-22 pubmed publisher
    ..In this study, for the imaging of HER2-related tumours, a modified RNA aptamer with HER2-specific targeting was labelled with (99m)Tc, by using hydrazino nicotinamide (HYNIC) as the ..
  56. Esvelt K, Mali P, Braff J, Moosburner M, Yaung S, Church G. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods. 2013;10:1116-21 pubmed publisher
    The Cas9 protein from the Streptococcus pyogenes CRISPR-Cas acquired immune system has been adapted for both RNA-guided genome editing and gene regulation in a variety of organisms, but it can mediate only a single activity at a time ..
  57. Zheng K, Xiao S, Liu J, Zhang J, Hao Y, Tan Z. Co-transcriptional formation of DNA:RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control. Nucleic Acids Res. 2013;41:5533-41 pubmed publisher
    ..Here, we report an almost entirely neglected, but actually much more prevalent form of G-quadruplexes, DNA:RNA hybrid G-quadruplexes (HQ) that forms in transcription...
  58. Norbury C. Cytoplasmic RNA: a case of the tail wagging the dog. Nat Rev Mol Cell Biol. 2013;14:643-53 pubmed publisher
    ..roles for cytoplasmic poly(A) polymerase-related enzymes that add uridylyl, rather than adenylyl, residues to RNA 3' ends have also emerged...
  59. Behr J, Kahles A, Zhong Y, Sreedharan V, Drewe P, Rätsch G. MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. Bioinformatics. 2013;29:2529-38 pubmed publisher
    High-throughput sequencing of mRNA (RNA-Seq) has led to tremendous improvements in the detection of expressed genes and reconstruction of RNA transcripts...
  60. Fustin J, Doi M, Yamaguchi Y, Hida H, Nishimura S, Yoshida M, et al. RNA-methylation-dependent RNA processing controls the speed of the circadian clock. Cell. 2013;155:793-806 pubmed publisher
    ..Here, we report that inhibition of transmethylation reactions elongates the circadian period. RNA sequencing then reveals methylation inhibition causes widespread changes in the transcription of the RNA processing ..
  61. Wang Y, Wang Z, Tanaka Hall T. Engineered proteins with Pumilio/fem-3 mRNA binding factor scaffold to manipulate RNA metabolism. FEBS J. 2013;280:3755-67 pubmed publisher
    Pumilio/fem-3 mRNA binding factor proteins are characterized by a sequence-specific RNA-binding domain...
  62. Yuan C, Liu Y, Yang M, Liao D. New methods as alternative or corrective measures for the pitfalls and artifacts of reverse transcription and polymerase chain reactions (RT-PCR) in cloning chimeric or antisense-accompanied RNA. RNA Biol. 2013;10:958-67 pubmed publisher
    ..transcription (RT) and soon proceed with the synthesis of the second cDNA strand, avoiding manipulations of fragile RNA. Our 3'-end cloning method does not involve poly-dT primers and polymerase chain reactions (PCR), is low in ..
  63. Vik E, Nawaz M, Strøm Andersen P, Fladeby C, Bjørås M, Dalhus B, et al. Endonuclease V cleaves at inosines in RNA. Nat Commun. 2013;4:2271 pubmed publisher
    ..V (ENDOV) and also Escherichia coli endonuclease V are highly active ribonucleases specific for inosine in RNA. Inosines are normal residues in certain RNAs introduced by specific deaminases...
  64. Kuprys P, Davis S, Hauer T, Meltser M, Tzfati Y, Kirk K. Identification of telomerase RNAs from filamentous fungi reveals conservation with vertebrates and yeasts. PLoS ONE. 2013;8:e58661 pubmed publisher
    ..by the ribonucleoprotein telomerase, which comprises a telomerase reverse transcriptase (TERT) and a telomerase RNA (TER). TER contains a template for telomeric DNA synthesis...
  65. Ostalecki C, Konrad A, Thurau E, Schuler G, Croner R, Pommer A, et al. Combined multi-gene analysis at the RNA and protein levels in single FFPE tissue sections. Exp Mol Pathol. 2013;95:1-6 pubmed publisher
    ..of individualized medicine require rapid analyses of comprehensive multi-gene expression patterns both at the RNA and protein levels...
  66. Sokolowski R, Graham S, White M. Cas6 specificity and CRISPR RNA loading in a complex CRISPR-Cas system. Nucleic Acids Res. 2014;42:6532-41 pubmed publisher
    ..In type I and type III CRISPR-Cas systems, CRISPR RNA (crRNA) is generated by cleavage of a primary transcript by the Cas6 endonuclease and loaded into multisubunit ..
  67. Aghaeepour N, Hoos H. Ensemble-based prediction of RNA secondary structures. BMC Bioinformatics. 2013;14:139 pubmed publisher
    Accurate structure prediction methods play an important role for the understanding of RNA function...
  68. Geng R, Yuan C, Chen Y. Exploring differentially expressed genes by RNA-Seq in cashmere goat (Capra hircus) skin during hair follicle development and cycling. PLoS ONE. 2013;8:e62704 pubmed publisher
    ..profiling of skin was carried out by analysing samples from three hair follicle developmental stages using RNA-Seq...
  69. Sharif H, Ozgur S, Sharma K, Basquin C, Urlaub H, Conti E. Structural analysis of the yeast Dhh1-Pat1 complex reveals how Dhh1 engages Pat1, Edc3 and RNA in mutually exclusive interactions. Nucleic Acids Res. 2013;41:8377-90 pubmed publisher
    ..Pat1 and Edc3 also interfere and compete with the RNA-binding properties of Dhh1...
  70. Wunderlich C, Huber R, Spitzer R, Liedl K, Kloiber K, Kreutz C. A novel paramagnetic relaxation enhancement tag for nucleic acids: a tool to study structure and dynamics of RNA. ACS Chem Biol. 2013;8:2697-706 pubmed publisher
    ..relaxation enhancement induced by the nitroxide radical to discern two folding states in a bistable RNA. Finally, we investigated the fast conformational sampling of the HIV-1 TAR RNA, a paradigm for structural ..
  71. Bazinet A, Cummings M, Mitter K, Mitter C. Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study. PLoS ONE. 2013;8:e82615 pubmed publisher
    ..We used transcriptome RNA-Seq to generate 1579 putatively orthologous gene sequences across a broad sample of 40 apoditrysians plus four ..
  72. Meier M, Patel T, Booy E, Marushchak O, Okun N, Deo S, et al. Binding of G-quadruplexes to the N-terminal recognition domain of the RNA helicase associated with AU-rich element (RHAU). J Biol Chem. 2013;288:35014-27 pubmed publisher
    ..b>RNA helicase associated with AU-rich element (RHAU), a member of the ATP-dependent DEX(H/D) family of RNA helicases, ..
  73. Yu C, Teulade Fichou M, Olsthoorn R. Stimulation of ribosomal frameshifting by RNA G-quadruplex structures. Nucleic Acids Res. 2014;42:1887-92 pubmed publisher
    ..motifs have been extensively studied on the DNA level; however, exploration of the biological roles of G4s at the RNA level is just emerging...