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. Robinson K, Orans J, Kovach A, Link T, Brennan R. Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching. Nucleic Acids Res. 2014;42:2736-49 pubmed publisher
    Hfq is a posttranscriptional riboregulator and RNA chaperone that binds small RNAs and target mRNAs to effect their annealing and message-specific regulation in response to environmental stressors...
  5. 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...
  6. Teplova M, Hafner M, Teplov D, Essig K, Tuschl T, Patel D. Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites. Genes Dev. 2013;27:928-40 pubmed publisher
    ..and its Caenorhabditis elegans homolog, GLD-1 (defective in germ line development), are evolutionarily conserved RNA-binding proteins, which post-transcriptionally regulate target genes essential for developmental processes and ..
  7. Surana P, Satchidanandam V, Nair D. RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state. Nucleic Acids Res. 2014;42:2758-73 pubmed publisher
    Flaviviral RNA-dependent RNA polymerases (RdRps) initiate replication of the single-stranded RNA genome in the absence of a primer. The template sequence 5'-CU-3' at the 3'-end of the flaviviral genome is highly conserved...
  8. Zhu M, Dahmen J, Stacey G, Cheng J. Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data. BMC Bioinformatics. 2013;14:278 pubmed publisher
    High-throughput RNA sequencing (RNA-Seq) is a revolutionary technique to study the transcriptome of a cell under various conditions at a systems level...
  9. 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) ..

More Information

Publications101 found, 100 shown here

  1. 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...
  2. 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...
  3. 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 ..
  4. Binning J, Wang T, Luthra P, Shabman R, Borek D, Liu G, et al. Development of RNA aptamers targeting Ebola virus VP35. Biochemistry. 2013;52:8406-19 pubmed publisher
    ..Taken together, our results support the identification of two aptamers that bind filoviral VP35 proteins with high affinity and specificity and have the capacity to potentially function as filoviral VP35 protein inhibitors. ..
  5. Hoskins J, Ofori L, Chen C, Kumar A, Sobczak K, Nakamori M, et al. Lomofungin and dilomofungin: inhibitors of MBNL1-CUG RNA binding with distinct cellular effects. Nucleic Acids Res. 2014;42:6591-602 pubmed publisher
    Myotonic dystrophy type 1 (DM1) is a dominantly inherited neuromuscular disorder resulting from expression of RNA containing an expanded CUG repeat (CUG(exp)). The pathogenic RNA is retained in nuclear foci...
  6. 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...
  7. 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 ..
  8. Aik W, Scotti J, Choi H, Gong L, Demetriades M, Schofield C, et al. Structure of human RNA N⁶-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation. Nucleic Acids Res. 2014;42:4741-54 pubmed publisher
    ..and ferrous iron-dependent nucleic acid oxygenase (NAOX) that catalyzes the demethylation of N(6)-methyladenine in RNA. ALKBH5 is upregulated under hypoxia and plays a role in spermatogenesis...
  9. 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...
  10. Lukasiak P, Antczak M, Ratajczak T, Bujnicki J, Szachniuk M, Adamiak R, et al. RNAlyzer--novel approach for quality analysis of RNA structural models. Nucleic Acids Res. 2013;41:5978-90 pubmed publisher
    The continuously increasing amount of RNA sequence and experimentally determined 3D structure data drives the development of computational methods supporting exploration of these data...
  11. Sotelo J, Canclini L, Kun A, Sotelo Silveira J, Xu L, Wallrabe H, et al. Myosin-Va-dependent cell-to-cell transfer of RNA from Schwann cells to axons. PLoS ONE. 2013;8:e61905 pubmed publisher
    To better understand the role of protein synthesis in axons, we have identified the source of a portion of axonal RNA. We show that proximal segments of transected sciatic nerves accumulate newly-synthesized RNA in axons...
  12. Rahrig R, Petrov A, Leontis N, Zirbel C. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures. Nucleic Acids Res. 2013;41:W15-21 pubmed publisher
    The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures...
  13. Ihara R, Matsukawa K, Nagata Y, Kunugi H, Tsuji S, Chihara T, et al. RNA binding mediates neurotoxicity in the transgenic Drosophila model of TDP-43 proteinopathy. Hum Mol Genet. 2013;22:4474-84 pubmed publisher
    ..The discovery of mutations in the gene encoding an RNA-binding protein, TAR DNA-binding protein of 43 kD (TDP-43), in familial ALS, strongly implicated abnormalities in ..
  14. Li H, Wang Z, Zhou X, Cheng Y, Xie Z, Manley J, et al. Far upstream element-binding protein 1 and RNA secondary structure both mediate second-step splicing repression. Proc Natl Acad Sci U S A. 2013;110:E2687-95 pubmed publisher
    ..Importantly, we identified far upstream element-binding protein 1 (FUBP1), a single-stranded DNA- and RNA-binding protein not previously implicated in splicing, as a strong ESS binding protein, and several assays ..
  15. Lipscombe D, Allen S, Toro C. Control of neuronal voltage-gated calcium ion channels from RNA to protein. Trends Neurosci. 2013;36:598-609 pubmed publisher
    ..we highlight recent studies that delineate mechanisms controlling the expression of CaV channels at the level of RNA and protein...
  16. Qiu M, Khisamutdinov E, Zhao Z, Pan C, Choi J, Leontis N, et al. RNA nanotechnology for computer design and in vivo computation. Philos Trans A Math Phys Eng Sci. 2013;371:20120310 pubmed publisher
    ..Recently, RNA nanotechnology has emerged as an alternative approach...
  17. Li J, Church G. Deciphering the functions and regulation of brain-enriched A-to-I RNA editing. Nat Neurosci. 2013;16:1518-22 pubmed publisher
    Adenosine-to-inosine (A-to-I) RNA editing, in which genomically encoded adenosine is changed to inosine in RNA, is catalyzed by adenosine deaminase acting on RNA (ADAR)...
  18. Mackness B, Tran M, McClain S, Matthews C, Zitzewitz J. Folding of the RNA recognition motif (RRM) domains of the amyotrophic lateral sclerosis (ALS)-linked protein TDP-43 reveals an intermediate state. J Biol Chem. 2014;289:8264-76 pubmed publisher
    Pathological alteration of TDP-43 (TAR DNA-binding protein-43), a protein involved in various RNA-mediated processes, is a hallmark feature of the neurodegenerative diseases amyotrophic lateral sclerosis and frontotemporal lobar ..
  19. Martadinata H, Phan A. Formation of a stacked dimeric G-quadruplex containing bulges by the 5'-terminal region of human telomerase RNA (hTERC). Biochemistry. 2014;53:1595-600 pubmed publisher
    We investigate the structure formed by the first 18-nt of the 5'-terminal region of the human telomerase RNA (hTERC or hTR) using gel electrophoresis and UV, CD, and NMR spectroscopy...
  20. 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...
  21. Zhang C, Lee K, Swanson M, Darnell R. Prediction of clustered RNA-binding protein motif sites in the mammalian genome. Nucleic Acids Res. 2013;41:6793-807 pubmed publisher
    Sequence-specific interactions of RNA-binding proteins (RBPs) with their target transcripts are essential for post-transcriptional gene expression regulation in mammals...
  22. 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...
  23. 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...
  24. 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...
  25. 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 ..
  26. 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 ..
  27. 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. ..
  28. 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...
  29. 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...
  30. 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...
  31. 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...
  32. 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...
  33. 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...
  34. 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...
  35. 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...
  36. 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...
  37. 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. ..
  38. 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"...
  39. 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 ..
  40. 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...
  41. 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, ..
  42. 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...
  43. 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...
  44. 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...
  45. 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...
  46. 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...
  47. 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...
  48. 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...
  49. 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 ..
  50. 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.
  51. 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...
  52. 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)...
  53. 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...
  54. 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...
  55. 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...
  56. 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, ..
  57. 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...
  58. 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...
  59. 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...
  60. 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 ..
  61. 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...
  62. 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)...
  63. 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...
  64. 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 ..
  65. 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'...
  66. 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...
  67. 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...
  68. 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...
  69. 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 ..
  70. 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...
  71. 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 ..
  72. 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...
  73. 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...
  74. 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
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    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...
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    Recent work, including large-scale genetic and molecular analyses, identified RNA-binding proteins (RBPs) as major players in the prevention of genome instability...
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    ..by the ribonucleoprotein telomerase, which comprises a telomerase reverse transcriptase (TERT) and a telomerase RNA (TER). TER contains a template for telomeric DNA synthesis...
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    ..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 ..
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    ..motifs have been extensively studied on the DNA level; however, exploration of the biological roles of G4s at the RNA level is just emerging...
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