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. doi Mapping and quantifying mammalian transcriptomes by RNA-Seq
    Ali Mortazavi
    Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Nat Methods 5:621-8. 2008
  2. pmc Full-length transcriptome assembly from RNA-Seq data without a reference genome
    Manfred G Grabherr
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:644-52. 2011
  3. pmc RNA-guided human genome engineering via Cas9
    Prashant Mali
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Science 339:823-6. 2013
  4. pmc Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    Jo Vandesompele
    Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, B 9000 Ghent, Belgium
    Genome Biol 3:RESEARCH0034. 2002
  5. pmc RNA-Seq: a revolutionary tool for transcriptomics
    Zhong Wang
    Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, Connecticut 06520, USA
    Nat Rev Genet 10:57-63. 2009
  6. pmc tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    T M Lowe
    Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA
    Nucleic Acids Res 25:955-64. 1997
  7. doi A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
    Martin Jinek
    Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Science 337:816-21. 2012
  8. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
  9. pmc RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
    Bo Li
    Department of Computer Sciences, University of Wisconsin Madison, Madison, WI, USA
    BMC Bioinformatics 12:323. 2011
  10. pmc De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
    Brian J Haas
    Broad Institute of Massachusetts Institute of Technology MIT, Cambridge, Massachusetts, USA
    Nat Protoc 8:1494-512. 2013

Detail Information

Publications362 found, 100 shown here

  1. doi Mapping and quantifying mammalian transcriptomes by RNA-Seq
    Ali Mortazavi
    Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Nat Methods 5:621-8. 2008
    ..by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq)...
  2. pmc Full-length transcriptome assembly from RNA-Seq data without a reference genome
    Manfred G Grabherr
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:644-52. 2011
    ..Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome...
  3. pmc RNA-guided human genome engineering via Cas9
    Prashant Mali
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Science 339:823-6. 2013
    ..clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign nucleic acids...
  4. pmc Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    Jo Vandesompele
    Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, B 9000 Ghent, Belgium
    Genome Biol 3:RESEARCH0034. 2002
  5. pmc RNA-Seq: a revolutionary tool for transcriptomics
    Zhong Wang
    Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, Connecticut 06520, USA
    Nat Rev Genet 10:57-63. 2009
    b>RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes...
  6. pmc tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    T M Lowe
    Department of Genetics, Washington University School of Medicine, 660 South Euclid, Box 8232, St Louis, MO 63110, USA
    Nucleic Acids Res 25:955-64. 1997
    We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases...
  7. doi A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
    Martin Jinek
    Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Science 337:816-21. 2012
    ..in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA...
  8. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
    ..The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large...
  9. pmc RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
    Bo Li
    Department of Computer Sciences, University of Wisconsin Madison, Madison, WI, USA
    BMC Bioinformatics 12:323. 2011
    b>RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms...
  10. pmc De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
    Brian J Haas
    Broad Institute of Massachusetts Institute of Technology MIT, Cambridge, Massachusetts, USA
    Nat Protoc 8:1494-512. 2013
    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 ..
  11. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
    ..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
  12. pmc Infernal 1.0: inference of RNA alignments
    Eric P Nawrocki
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Bioinformatics 25:1335-7. 2009
    INFERNAL builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence- and structure-based multiple sequence ..
  13. pmc A scaling normalization method for differential expression analysis of RNA-seq data
    Mark D Robinson
    Bioinformatics Division, Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Australia
    Genome Biol 11:R25. 2010
    The fine detail provided by sequencing-based transcriptome surveys suggests that RNA-seq is likely to become the platform of choice for interrogating steady state RNA...
  14. pmc Rfam: updates to the RNA families database
    Paul P Gardner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    Nucleic Acids Res 37:D136-40. 2009
    Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs)...
  15. ncbi Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction
    P Chomczynski
    Anal Biochem 162:156-9. 1987
    A new method of total RNA isolation by a single extraction with an acid guanidinium thiocyanate-phenol-chloroform mixture is described...
  16. doi DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
    Likun Wang
    MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST Department of Automation, Tsinghua, University, Beijing 100084, China
    Bioinformatics 26:136-8. 2010
    High-throughput RNA sequencing (RNA-seq) is rapidly emerging as a major quantitative transcriptome profiling platform...
  17. pmc Computation for ChIP-seq and RNA-seq studies
    Shirley Pepke
    Center for Advanced Computing Research, California Institute of Technology, Pasadena, California, USA
    Nat Methods 6:S22-32. 2009
    ..of protein-DNA interactions and transcriptomes are increasingly done by deep DNA sequencing methods (ChIP-seq and RNA-seq)...
  18. pmc Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    Mitchell Guttman
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 458:223-7. 2009
    ..Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes...
  19. ncbi Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends
    Claus M Azzalin
    Swiss Institute for Experimental Cancer Research ISREC, CH 1066 Epalinges, Switzerland
    Science 318:798-801. 2007
    ..We demonstrate that mammalian telomeres are transcribed into telomeric repeat-containing RNA (TERRA)...
  20. pmc A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?
    Leonardo Salmena
    Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
    Cell 146:353-8. 2011
    ..We propose that this "competing endogenous RNA" (ceRNA) activity forms a large-scale regulatory network across the transcriptome, greatly expanding the functional ..
  21. pmc RNAstructure: software for RNA secondary structure prediction and analysis
    Jessica S Reuter
    Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA
    BMC Bioinformatics 11:129. 2010
    To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides...
  22. pmc Statistical inferences for isoform expression in RNA-Seq
    Hui Jiang
    Institute for Computational and Mathematical Engineering and Department of Statistics, Stanford University, Stanford, CA 94305, USA
    Bioinformatics 25:1026-32. 2009
    The development of RNA sequencing (RNA-Seq) makes it possible for us to measure transcription at an unprecedented precision and throughput...
  23. doi Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome
    Zhiyu Peng
    BGI Shenzhen, Shenzhen, China
    Nat Biotechnol 30:253-60. 2012
    b>RNA editing is a post-transcriptional event that recodes hereditary information...
  24. pmc Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
    Gregory R Grant
    Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Bioinformatics 27:2518-28. 2011
    ..Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing...
  25. ncbi Extension of life-span by introduction of telomerase into normal human cells
    A G Bodnar
    Geron Corporation, Menlo Park, CA 94025, USA
    Science 279:349-52. 1998
    ..The ability to maintain normal human cells in a phenotypically youthful state could have important applications in research and medicine...
  26. pmc The Vienna RNA websuite
    Andreas R Gruber
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Wien, Austria
    Nucleic Acids Res 36:W70-4. 2008
    The Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. It provides a web interface to the most commonly used programs of the Vienna RNA package...
  27. pmc DNA interrogation by the CRISPR RNA-guided endonuclease Cas9
    Samuel H Sternberg
    1 Department of Chemistry, University of California, Berkeley, California 94720, USA 2
    Nature 507:62-7. 2014
    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...
  28. pmc Infernal 1.1: 100-fold faster RNA homology searches
    Eric P Nawrocki
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Bioinformatics 29:2933-5. 2013
    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...
  29. pmc The RIN: an RNA integrity number for assigning integrity values to RNA measurements
    Andreas Schroeder
    Agilent Technologies, Hewlett Packard Strasse 8, 76337 Waldbronn, Germany
    BMC Mol Biol 7:3. 2006
    The integrity of RNA molecules is of paramount importance for experiments that try to reflect the snapshot of gene expression at the moment of RNA extraction...
  30. doi Natural RNA circles function as efficient microRNA sponges
    Thomas B Hansen
    Department of Molecular Biology and Genetics, Aarhus University, C F Møllers Allé 3, 8000C, Aarhus, Denmark
    Nature 495:384-8. 2013
    ..has been shown to be affected by the presence of miRNA sponge transcripts, the so-called competing endogenous RNA in humans and target mimicry in plants...
  31. pmc Detecting differential usage of exons from RNA-seq data
    Simon Anders
    European Molecular Biology Laboratory, 69111 Heidelberg, Germany
    Genome Res 22:2008-17. 2012
    b>RNA-seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression...
  32. ncbi Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs
    Gunter Meister
    Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10021, USA
    Mol Cell 15:185-97. 2004
    ..Exogenously introduced siRNAs also associate with Ago2 for guiding target RNA cleavage...
  33. ncbi RNA integrity and the effect on the real-time qRT-PCR performance
    Simone Fleige
    Physiology Weihenstephan, Center of Life and Food Sciences ZIEL, Technical University of Munich, 85350 Freising, Germany
    Mol Aspects Med 27:126-39. 2006
    The assessment of RNA integrity is a critical first step in obtaining meaningful gene expression data...
  34. doi UNAFold: software for nucleic acid folding and hybridization
    Nicholas R Markham
    Xerox Litigation Services, Albany, NY, USA
    Methods Mol Biol 453:3-31. 2008
    ..Folding (secondary structure) prediction for single-stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling...
  35. ncbi Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA
    A E Pasquinelli
    Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston 02114, USA
    Nature 408:86-9. 2000
    ..Transition from the first to the second larval stage fates requires the 22-nucleotide lin-4 RNA, and transition from late larval to adult cell fates requires the 21-nucleotide let-7 RNA...
  36. pmc RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions
    Blake Wiedenheft
    Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 108:10092-7. 2011
    Prokaryotes have evolved multiple versions of an RNA-guided adaptive immune system that targets foreign nucleic acids...
  37. pmc DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration
    Hiroki Kaneko
    Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, Kentucky 40506, USA
    Nature 471:325-30. 2011
    ..DICER1 knockdown induces accumulation of Alu RNA in human RPE cells and Alu-like B1 and B2 RNAs in mouse RPE...
  38. pmc RNA toxicity from the ALS/FTD C9ORF72 expansion is mitigated by antisense intervention
    Christopher J Donnelly
    Department of Neurology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2 270, Baltimore, MD 21205, USA Brain Science Institute, Johns Hopkins University, 855 N Wolfe Street, Rangos 2 270, Baltimore, MD 21205, USA
    Neuron 80:415-28. 2013
    ..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) ..
  39. pmc Comparative analysis of RNA sequencing methods for degraded or low-input samples
    Xian Adiconis
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Methods 10:623-9. 2013
    b>RNA-seq is an effective method for studying the transcriptome, but it can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations or cadavers...
  40. doi Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex
    Debora Lika Makino
    Department of Structural Cell Biology, MPI for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Nature 495:70-5. 2013
    The exosome is the major 3'-5' RNA-degradation complex in eukaryotes. The ubiquitous core of the yeast exosome (Exo-10) is formed by nine catalytically inert subunits (Exo-9) and a single active RNase, Rrp44...
  41. ncbi The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression
    Christophe Maris
    Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, Zurich, Switzerland
    FEBS J 272:2118-31. 2005
    The RNA recognition motif (RRM), also known as RNA-binding domain (RBD) or ribonucleoprotein domain (RNP) is one of the most abundant protein domains in eukaryotes...
  42. pmc The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA
    Philipp Kapranov
    Helicos BioSciences Corporation, One Kendall Square, Building 700, Cambridge, MA 02139, USA
    BMC Biol 8:149. 2010
    ..However, the fraction of all cellular RNA whose function we do not understand and the fraction of the genome that is utilized to produce that RNA remain ..
  43. doi RSeQC: quality control of RNA-seq experiments
    Liguo Wang
    Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
    Bioinformatics 28:2184-5. 2012
    b>RNA-seq has been extensively used for transcriptome study. Quality control (QC) is critical to ensure that RNA-seq data are of high quality and suitable for subsequent analyses...
  44. pmc MODOMICS: a database of RNA modification pathways--2013 update
    Magdalena A Machnicka
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul ks Trojdena 4, PL 02 109 Warsaw, Poland
    Nucleic Acids Res 41:D262-7. 2013
    MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in ..
  45. doi RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing
    Brian T Wilhelm
    Laboratory of Molecular Genetics of Stem Cells, C P 6128 Succursale Centre Ville, Montreal, Que H3C3J7, Canada
    Methods 48:249-57. 2009
    ..One such method that has recently been developed uses MPS technology to directly survey the RNA content of cells, without requiring any of the traditional cloning associated with EST sequencing...
  46. pmc Analysis and design of RNA sequencing experiments for identifying isoform regulation
    Yarden Katz
    Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology MIT, Cambridge, Massachusetts, USA
    Nat Methods 7:1009-15. 2010
    ..To infer isoform regulation from high-throughput sequencing of cDNA fragments (RNA-seq), we developed the mixture-of-isoforms (MISO) model, a statistical model that estimates expression of ..
  47. doi G-quadruplexes in RNA biology
    Stefania Millevoi
    INSERM UMR 1037, University of Toulouse III, Cancer Research Center of Toulouse, Toulouse 31432, Cedex 4, France
    Wiley Interdiscip Rev RNA 3:495-507. 2012
    G-quadruplexes are noncanonical structures formed by G-rich DNA and RNA sequences that fold into a four-stranded conformation...
  48. pmc ExoCarta 2012: database of exosomal proteins, RNA and lipids
    Suresh Mathivanan
    Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
    Nucleic Acids Res 40:D1241-4. 2012
    ..ExoCarta (http://www.exocarta.org) is a manually curated database of exosomal proteins, RNA and lipids. The database catalogs information from both published and unpublished exosomal studies...
  49. pmc RNA polymerase III detects cytosolic DNA and induces type I interferons through the RIG-I pathway
    Yu Hsin Chiu
    Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390 9148, USA
    Cell 138:576-91. 2009
    ..mitochondrial antiviral signaling (MAVS) proteins mediate IFN production in response to cytosolic double-stranded RNA or single-stranded RNA containing 5'-triphosphate (5'-ppp)...
  50. pmc Converging mechanisms in ALS and FTD: disrupted RNA and protein homeostasis
    Shuo Chien Ling
    Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093 0670, USA
    Neuron 79:416-38. 2013
    ..Dysfunction in RNA processing and protein homeostasis is an emerging theme...
  51. pmc Orthogonal Cas9 proteins for RNA-guided gene regulation and editing
    Kevin M Esvelt
    1 Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA 2
    Nat Methods 10:1116-21. 2013
    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 ..
  52. pmc Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction
    Stephen A Bustin
    Centre for Academic Surgery Institute of Cell and Molecular Science Barts, University of London, UK
    J Biomol Tech 15:155-66. 2004
    Polymerase chain reaction (PCR)-based assays can target either DNA (the genome) or RNA (the transcriptome). Targeting the genome generates robust data that are informative and, most importantly, generally applicable...
  53. pmc Incorporating RNA-seq data into the zebrafish Ensembl genebuild
    John E Collins
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
    Genome Res 22:2067-78. 2012
    ..of gene models is improved by increasing the species-specific component that can be cost-effectively achieved using RNA-seq. Two zebrafish gene annotations are presented in Ensembl version 62 built on the Zv9 reference sequence...
  54. pmc De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology
    Jacob E Crawford
    Department of Entomology, Cornell University, Ithaca, New York, United States of America
    PLoS ONE 5:e14202. 2010
    ..funestus from a newly founded colony in Burkina Faso, West Africa, using the Illumina GAIIx next generation sequencing platform...
  55. pmc Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
    Chaolin Zhang
    Laboratory of Molecular Neuro Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
    Nat Biotechnol 29:607-14. 2011
    Mammalian RNA complexity is regulated through interactions of RNA-binding proteins (RBPs) with their target transcripts...
  56. pmc Uncovering the complexity of transcriptomes with RNA-Seq
    Valerio Costa
    Institute of Genetics and Biophysics A Buzzati Traverso, IGB CNR, Naples, Italy
    J Biomed Biotechnol 2010:853916. 2010
    ..b>RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction, CNV-Seq for large genome nucleotide ..
  57. doi R loops: from transcription byproducts to threats to genome stability
    Andres Aguilera
    CABIMER, Universidad de Sevilla CSIC, Av Americo Vespucio s n, 41092 Sevilla, Spain
    Mol Cell 46:115-24. 2012
    b>RNA:DNA hybrid structures known as R loops were thought to be rare byproducts of transcription...
  58. pmc RNAalifold: improved consensus structure prediction for RNA alignments
    Stephan H Bernhart
    Department of Computer Science, University of Leipzig, Leipzig, Germany
    BMC Bioinformatics 9:474. 2008
    ..In recent years, several alternative approaches have been advocated, pointing to several shortcomings of the original RNAalifold approach...
  59. pmc Functions and regulation of RNA editing by ADAR deaminases
    Kazuko Nishikura
    Department of Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania 19104 4268, USA
    Annu Rev Biochem 79:321-49. 2010
    One type of RNA editing converts adenosines to inosines (A-->I editing) in double-stranded RNA (dsRNA) substrates. A-->I RNA editing is mediated by adenosine deaminase acting on RNA (ADAR) enzymes...
  60. pmc VARNA: Interactive drawing and editing of the RNA secondary structure
    Kévin Darty
    LRI, UMR CNRS 8623, UMR CNRS 8621, Universite Paris Sud 11, F91405 Orsay Cedex, France
    Bioinformatics 25:1974-5. 2009
    VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
  61. pmc Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 456:921-6. 2008
    ..Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-nucleotide guide DNA and a 20-nucleotide target RNA containing cleavage-preventing mismatches at the 10-11 step...
  62. pmc RNA processing and its regulation: global insights into biological networks
    Donny D Licatalosi
    Howard Hughes Medical Institute, Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, New York 10021, USA
    Nat Rev Genet 11:75-87. 2010
    ..of eukaryotic gene expression have been transformed by the finding that enormous diversity can be generated at the RNA level...
  63. doi RNA recognition motifs: boring? Not quite
    Antoine Cléry
    Institute for Molecular Biology and Biophysics, ETH Zurich, CH 8093 Zurich, Switzerland
    Curr Opin Struct Biol 18:290-8. 2008
    The RNA recognition motif (RRM) is one of the most abundant protein domains in eukaryotes...
  64. pmc Structures of Cas9 endonucleases reveal RNA-mediated conformational activation
    Martin Jinek
    Department of Biochemistry, University of Zurich, CH 8057 Zurich, Switzerland
    Science 343:1247997. 2014
    Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune ..
  65. pmc Local RNA translation at the synapse and in disease
    Liqun Liu-Yesucevitz
    Department of Pharmacology, Boston University School of Medicine, Boston, Massachusetts 02118, USA
    J Neurosci 31:16086-93. 2011
    ..mRNA binding proteins (RBPs), such as FMRP, function as key regulators of local RNA translation, and the mTORC1 pathway acts as a primary signaling cascade for regulation of these proteins...
  66. doi The application of DNA and RNA G-quadruplexes to therapeutic medicines
    Gavin W Collie
    CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, UK WC1N 1AX
    Chem Soc Rev 40:5867-92. 2011
    ..We will highlight the similarities and differences between DNA and RNA folded G-quadruplexes in terms of stability, distribution, and exploitability as small molecule targets...
  67. pmc 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer
    Yan W Asmann
    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
    BMC Genomics 10:531. 2009
    ..Currently there are two protocols: full-length RNA sequencing (RNA-SEQ) and 3'-tag digital gene expression (DGE)...
  68. doi Prediction of protein-RNA binding sites by a random forest method with combined features
    Zhi Ping Liu
    Key Laboratory of Systems Biology, SIBS Novo Nordisk Translational Research Centre for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Bioinformatics 26:1616-22. 2010
    Protein-RNA interactions play a key role in a number of biological processes, such as protein synthesis, mRNA processing, mRNA assembly, ribosome function and eukaryotic spliceosomes...
  69. pmc Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers
    Johan Skog
    Department of Neurology, Massachusetts General Hospital, and Neuroscience Program, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA
    Nat Cell Biol 10:1470-6. 2008
    ..Messenger RNA mutant/variants and miRNAs characteristic of gliomas could be detected in serum microvesicles of glioblastoma ..
  70. pmc RNA sequencing: advances, challenges and opportunities
    Fatih Ozsolak
    Helicos BioSciences Corporation, One Kendall Square, Cambridge, Massachusetts 02139, USA
    Nat Rev Genet 12:87-98. 2011
    In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes...
  71. pmc Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers
    Alberto Perez
    Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica and Instituto Nacional de Bioinformatica, Parc Cientific de Barcelona, Barcelona 08028, Spain
    Biophys J 92:3817-29. 2007
    ..The total simulation time used to validate the force field includes near 1 mus of state-of-the-art molecular dynamics simulations in aqueous solution...
  72. pmc Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping
    Yuanchao Xue
    Wuhan University, Hubei, China
    Mol Cell 36:996-1006. 2009
    ..indicates that > 90% of human genes undergo alternative splicing, underscoring the contribution of differential RNA processing to diverse proteomes in higher eukaryotic cells...
  73. pmc Geometric nomenclature and classification of RNA base pairs
    N B Leontis
    Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Ohio 43403, USA
    RNA 7:499-512. 2001
    Non-Watson-Crick base pairs mediate specific interactions responsible for RNA-RNA self-assembly and RNA-protein recognition...
  74. pmc Vienna RNA secondary structure server
    Ivo L Hofacker
    Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, A 1090 Wien, Austria
    Nucleic Acids Res 31:3429-31. 2003
    The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures...
  75. pmc From RNA-seq reads to differential expression results
    Alicia Oshlack
    Bioinformatics Division, Walter and Eliza Hall Institute, 1G Royal Parade, Parkville 3052, Australia
    Genome Biol 11:220. 2010
    Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.
  76. pmc Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9
    Jian Feng Li
    Nat Biotechnol 31:688-91. 2013
  77. doi ExoCarta: A compendium of exosomal proteins and RNA
    Suresh Mathivanan
    Joint ProteomicS Laboratory, Ludwig Institute for Cancer Research and The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
    Proteomics 9:4997-5000. 2009
    ..Here, we describe ExoCarta, a compendium for proteins and RNA molecules identified in exosomes...
  78. pmc Accurate SHAPE-directed RNA structure determination
    Katherine E Deigan
    Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599 3290, USA
    Proc Natl Acad Sci U S A 106:97-102. 2009
    ..Deducing these structure-function relationships requires that it be possible to predict RNA secondary structures accurately...
  79. pmc Modeling non-uniformity in short-read rates in RNA-Seq data
    Jun Li
    Department of Statistics, Stanford University, Sequoia Hall, 390 Serra Mall, Stanford, CA 94305, USA
    Genome Biol 11:R50. 2010
    After mapping, RNA-Seq data can be summarized by a sequence of read counts commonly modeled as Poisson variables with constant rates along each transcript, which actually fit data poorly...
  80. ncbi Facile means for quantifying microRNA expression by real-time PCR
    Rui Shi
    North Carolina State University, Raleigh, NC 27695 7247, USA
    Biotechniques 39:519-25. 2005
    ..Here we report a simple and sensitive real-time PCR method for quantifying the expression of plant miRNAs. Total RNA, including miRNAs, was polyadenylated and reverse-transcribed with a poly(T) adapter into cDNAs for real-time PCR ..
  81. pmc The RNA Modification Database, RNAMDB: 2011 update
    William A Cantara
    The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
    Nucleic Acids Res 39:D195-201. 2011
    Since its inception in 1994, The RNA Modification Database (RNAMDB, http://rna-mdb.cas.albany.edu/RNAmods/) has served as a focal point for information pertaining to naturally occurring RNA modifications...
  82. ncbi Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila
    Julius Brennecke
    Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
    Cell 128:1089-103. 2007
    ..Thus, sense piRNAs, formed following cleavage of transposon mRNAs may enhance production of antisense piRNAs, complementary to active elements, by directing cleavage of transcripts from master control loci...
  83. pmc Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions
    Ci Chu
    Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Mol Cell 44:667-78. 2011
    Long noncoding RNAs (lncRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown...
  84. pmc Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence
    Ekaterina Semenova
    Waksman Institute, Piscataway, NJ 08854, USA
    Proc Natl Acad Sci U S A 108:10098-103. 2011
    ..sequences) systems provide adaptive immunity against viruses when a spacer sequence of small CRISPR RNA (crRNA) matches a protospacer sequence in the viral genome...
  85. doi Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure
    E Meyer
    Integrative Biology Section, The University of Texas at Austin, Austin, TX 78712, USA
    Mol Ecol 20:3599-616. 2011
    ..Here, we applied a novel RNA-Seq protocol to study molecular responses to heat and settlement inducers in aposymbiotic larvae of the reef-..
  86. doi Exosome isolation for proteomic analyses and RNA profiling
    Douglas D Taylor
    James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA
    Methods Mol Biol 728:235-46. 2011
    ..Recently, we have demonstrated the presence of miRNAs within the RNA fraction of circulating tumor-derived exosomes...
  87. pmc Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
    Michal Rabani
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:436-42. 2011
    Cellular RNA levels are determined by the interplay of RNA production, processing and degradation...
  88. pmc Small RNA binding to the lateral surface of Hfq hexamers and structural rearrangements upon mRNA target recognition
    Evelyn Sauer
    Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Proc Natl Acad Sci U S A 109:9396-401. 2012
    ..Hfq forms hexameric rings, which preferably bind uridine-rich RNA 3' ends on their proximal surface and adenine-rich sequences on their distal surface...
  89. doi Organization of intracellular reactions with rationally designed RNA assemblies
    Camille J Delebecque
    Harvard Medical School, Department of Systems Biology, 200 Longwood Avenue, Boston, MA 02115, USA
    Science 333:470-4. 2011
    ..We designed and assembled multidimensional RNA structures and used them as scaffolds for the spatial organization of bacterial metabolism...
  90. ncbi Exporting RNA from the nucleus to the cytoplasm
    Alwin Köhler
    Biochemie Zentrum der Universitat Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
    Nat Rev Mol Cell Biol 8:761-73. 2007
    The transport of RNA molecules from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes via mobile export receptors...
  91. doi RNA targeting therapeutics: molecular mechanisms of antisense oligonucleotides as a therapeutic platform
    C Frank Bennett
    Isis Pharmaceuticals, Inc, Carlsbad, California 92008, USA
    Annu Rev Pharmacol Toxicol 50:259-93. 2010
    Dramatic advances in understanding of the roles RNA plays in normal health and disease have greatly expanded over the past 10 years and have made it clear that scientists are only beginning to comprehend the biology of RNAs...
  92. doi Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels
    Masato Kato
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, 75390 9152, USA
    Cell 149:753-67. 2012
    Eukaryotic cells contain assemblies of RNAs and proteins termed RNA granules. Many proteins within these bodies contain KH or RRM RNA-binding domains as well as low complexity (LC) sequences of unknown function...
  93. ncbi RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)
    Edward J Merino
    Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599 3290, USA
    J Am Chem Soc 127:4223-31. 2005
    The reactivity of an RNA ribose hydroxyl is shown to be exquisitely sensitive to local nucleotide flexibility because a conformationally constrained adjacent 3'-phosphodiester inhibits formation of the deprotonated, nucleophilic oxyanion ..
  94. doi Aptamers as therapeutics
    Anthony D Keefe
    X Chem Incorporated, 100 Beaver Street, Waltham, Massachusetts 02453, USA
    Nat Rev Drug Discov 9:537-50. 2010
    ..A series of aptamers currently in development may change how nucleic acid therapeutics are perceived. It is likely that in the future, aptamers will increasingly find use in concert with other therapeutic molecules and modalities...
  95. ncbi The transcriptional landscape of the mammalian genome
    P Carninci
    Science 309:1559-63. 2005
    ..The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development...
  96. pmc RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability
    Lamia Wahba
    Howard Hughes Medical Institute Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Mol Cell 44:978-88. 2011
    ..Studies in yeast and mammalian cells have shown that DSBs and instability can occur through RNA:DNA hybrids generated by defects in RNA elongation and splicing...
  97. doi RNA nucleotide methylation
    Yuri Motorin
    Laboratoire ARN RNP Maturation Structure Fonction, Enzymologie Moléculaire et Structurale AREMS, Universite Henri Poincare, Vandoeuvre les Nancy, France
    Wiley Interdiscip Rev RNA 2:611-31. 2011
    Methylation of RNA occurs at a variety of atoms, nucleotides, sequences and tertiary structures...
  98. doi Prediction of RNA secondary structure using generalized centroid estimators
    Michiaki Hamada
    Mizuho Information and Research Institute, Inc, 2 3 Kanda Nishikicho, Chiyoda ku, Tokyo 101 8443, Japan
    Bioinformatics 25:465-73. 2009
    ..However, there is room for improvement in the objective functions presented in previous studies, which are maximized in the posterior decoding with respect to the accuracy measures for secondary structures...
  99. doi Ribozyme-catalyzed transcription of an active ribozyme
    Aniela Wochner
    Medical Research Council MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Science 332:209-12. 2011
    A critical event in the origin of life is thought to have been the emergence of an RNA molecule capable of replicating a primordial RNA "genome...
  100. pmc Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq
    Guorong Xu
    Department of Computer Science, University of New Orleans, New Orleans, LA 70148, USA
    RNA 16:1610-22. 2010
  101. pmc Modelling and simulating generic RNA-Seq experiments with the flux simulator
    Thasso Griebel
    Bioinformatics and Genomics Program, Centre de Regulacio Genomica CRG, 08003 Barcelona, Spain
    Nucleic Acids Res 40:10073-83. 2012
    High-throughput sequencing of cDNA libraries constructed from cellular RNA complements (RNA-Seq) naturally provides a digital quantitative measurement for every expressed RNA molecule...

Research Grants82

    Lee Gehrke; Fiscal Year: 2002
    ..The immediate goals of the work are to define the biochemical basis of selective and competitive messenger RNA (mRNA) translation and to analyze the structure and function of specific ribonucleoprotein complexes...
  2. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..the Geronemo algorithm which we applied to yeast and uncovered a novel relationship between the sequence specific RNA factor PUF3 and P-Bodies, as well as a Single Nucleotide Polymorphism (SNP) in MKT1 that modulates this ..
  3. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying immune selection in M. tuberculosis. ..
  4. Regulation of HSV-1 Gene Expression and Replication by Nuclear Hormone Receptors
    SHAOCHUNG VICTOR HSIA; Fiscal Year: 2013
    ..RCC1/Ran complex is involved in the control of RNA translocation, DNA synthesis, and cell cycle progression via modulating effects on chromatin and nucleosomes...
  5. Mapping for Specialized Domains for FCeRI Signaling &Internalization
    Bridget S Wilson; Fiscal Year: 2013
    ..We will use RNA interference and transient transfection methods to disrupt the spectrin cortical network...
  6. Cardiotrophin-Like Cytokine 1, a Candidate Molecule for the FSGS Factor
    Virginia J Savin; Fiscal Year: 2010
    ..Preliminary studies show that anti-CLC-1 blocks the effect of FSGS serum and that glomeruli express RNA for receptor components...
  7. Pilot and definitive studies to evaluate Insertional Mutagenesis
    LU TAYLOR; Fiscal Year: 2012
    ..The following studies have been completed or are ongoing during FY 2006: RNA isolation for Toxicogenomic Variability Study: RNA is being isolated from sentinel Fischer 344 rats of varying ages ..
  8. Studies to Evaluate the Toxicological Potential of Test Articles
    LU TAYLOR; Fiscal Year: 2010
    ..The following studies have been completed or are ongoing during FY 2006: RNA isolation for Toxicogenomic Variability Study: RNA is being isolated from sentinel Fischer 344 rats of varying ages ..
  9. Ligand Directed Transdermal siRNA Delivery to Improve Wound Healing
    David M Evans; Fiscal Year: 2012
    ..Using RNA interference (RNAi) to down regulate a target gene expression, we have previously demonstrated that a multi-..
  10. Prevention of Acute Lung Injury by IL-6 activated STAT3
    Ana Moran; Fiscal Year: 2010
    ..Q-RT-PCR using amplified (a)RNA from laser capture micro-dissection (LCM)-isolated AECs and non(n)-AEC cells from sham, HS and HS/I rat lungs ..
  11. Targeting Galectin-3 with novel drugs for treatment of eczema
    Fu Tong Liu; Fiscal Year: 2010
    ..These molecules are a newly-established, but growing class of drugs called aptamers (RNA oligonucleotides), and may offer improved safety and specificity over traditional therapies...
  12. Gamma-Synuclein-Mediated Regulation of Norepinephrine Transporter
    Anita Sidhu; Fiscal Year: 2010
    ..Transcription and RNA labeling will be performed for 30 min in a reaction buffer containing 5 mM each of ATP, CTP, GTP, and 32P-UTP...
  13. Discovery of Small Molecule MBT Domain Antagonists
    STEPHEN VERNON FRYE; Fiscal Year: 2010
    ..1] The template upon which the epigenome is written is chromatin - the complex of histone proteins, RNA and DNA that efficiently package the genome in an appropriately accessible state within each cell...
  14. Lung Lysyl Oxidase Regulation by Metal Ion Homeostasis
    Wande Li; Fiscal Year: 2013
    ..to identify mechanisms for Cd silencing of the LO gene at the transcriptional level by examining Cd modulation of RNA polymerase II- directed LO pre-mRNA synthesis and processing, and of the LO promoter activation regulated by the ..
  15. Genetics and Haloperidol Response
    Robert J Hitzemann; Fiscal Year: 2012
    ..of the QTL and network based approaches using all possible methods but emphasizing viral mediated transfer of RNA interference...
  16. Med1 in Liver Metabolism, Regeneration and Cancer
    Janardan K Reddy; Fiscal Year: 2013
    ..The Mediator complex is necessary for the expression of RNA polymerase II (PoI II)-transcribed genes...
  17. Targeted siRNA nanotechnology for intravesical treatment of urologicaldiseases
    Robert M Weiss; Fiscal Year: 2010
    ..The Proof of Concept that we are testing is that intravesical instillation of small interference RNA (siRNA) packaged in biodegradable nanospheres provides wide opportunities for the treatment of urologic diseases ..
  18. Role of Polyamines in MYCN-Amplified Neuroblastoma
    ANDRE BACHMANN; Fiscal Year: 2009
    ..The proposed methods and techniques to pursue this work are: Northern blot, RT-PCR, nuclear run-ons, messenger RNA half-life studies, Western blot, yeast two-hybrid, co-immunoprecipitation, GST-pull down, site-directed mutagenesis,..
  19. Investigating Mechanism of Intracellular Rotational Transport with Optical T
    Jeffrey N Anker; Fiscal Year: 2012
    ..This inflammation and associated overproduction of reactive oxygen species further oxidize RNA/DNA/proteins, leading to fibrosis, mutagenesis and lung cancer...
    Terence S Dermody; Fiscal Year: 2013
    ..a fully plasmid-based reverse genetics system for reovirus, the first of its kind for any mammalian double-stranded RNA virus...
  21. Trichothecene Toxicity and the Ribotoxic Stress Response
    James J Pestka; Fiscal Year: 2012
    ..that: 1)deoxynivalenol (DON), a common foodborne trichothecene, mediates cleavage of 18S and 28S ribosomal (r)RNA, 2) double-stranded RNA-activated protein kinase (PKR), a ribosome-associated serine-threonine kinase, is essential ..
  22. Vitamin D and Estrogen Action in Bone: Concerted Role for hnRNPs in the C Family
    John S Adams; Fiscal Year: 2013
    ..of hnRNPs on the cells responsible for 1,25- dihydroxyvitamin D and estradiol-driven bone growth;2) employ new RNA immunoprecipitation and micro- RNA methodology to study the versatility of these hnRNPS to control transcript ..
  23. Vitamin D Hormone Signaling in Bone Mineral Homeostasis
    Mark R Haussler; Fiscal Year: 2010
    ..protein/enzyme complexes that either repress or induce DNA transcription by chromatin remodeling and linkage to RNA polymerase II...
  24. Tat and CDK9 on gene expression alterations coupled to HIV-1 Associated Dementia
    Xavier Grana; Fiscal Year: 2010
    ..This host complex is recruited by Tat to TAR, an RNA element in the nascent HIV-1 transcript, where CDK9 is positioned to phosphorylate RNA polymerase II (RNAPII) and ..
    Adrian R Krainer; Fiscal Year: 2010
    ..The specific aims are: 1. To study the mechanism of 5'-splice-site selection;2. To study RNA-binding proteins involved in 3'-splice-site recognition;3...
  26. Genomics of Antiviral Responses of Anopheles gambiae Against O'nyong-nyong Virus
    Young S Hong; Fiscal Year: 2010
    ..In ONNV- infected An. gambiae, hsc-70B expression was found to be highly induced, and RNA interference (RNAi) gene- silencing of hsc-70B increased ONNV titers in the mosquito...
  27. Mitochondrial dysfunction, oxidative stress, and surgical acute kidney injury
    ..potential, peroxisome proliferator-activated receptor [unreadable] coactivator 1-[unreadable] (PGC-1[unreadable]) RNA expression, and mtDNA copy number from isolated leukocytes and arterial lactate:pyruvate ratios), and clinical AKI (..
    Lisa M Salati; Fiscal Year: 2012
    ..course of our studies on mechanisms by which fatty acids regulate gene expression, we discovered that the rate of RNA splicing is inhibited in liver and primary hepatocytes by dietary polyunsaturated fat and by arachidonic acid, ..
  29. Steroid Responsive Mechanisms in the Ear
    DENNIS ROYAL TRUNE; Fiscal Year: 2012
    ..will be assessed with ELISA, Western blot, cytokine RNA expression, and quantitative RT-PCR...
  30. Regulation of microRNA-375 by cyclic-AMP in pancreatic beta-cells
    DAVID MATTHEW KELLER; Fiscal Year: 2010
    ..There is a growing awareness in [unreadable]- cell biology that small non-coding RNA molecules called microRNAs play a major role in development and physiology...
  31. Sex Steroid Hormone Regulation of Drug Reinforcement
    Diane Lebesgue; Fiscal Year: 2012
    ..We will then assess E2/G1 modulation of cocaine reinforcement in animals subjected to GPR30 knockdown using in vivo RNA interference targeted to the VTA...
  32. Identification and Analysis of Flavivirus Protease and RNA Helicase Inhibitors
    Radhakrishnan Padmanabhan; Fiscal Year: 2009
    ..Moreover, NS3 exhibits an RNA-stimulated NTPase, RNA helicase and the 5'-RNA triphosphatase (5'-RTPase) activities...
    Alvaro Puga; Fiscal Year: 2013
    ..These changes inhibit recruitment of RNA polymerase II to the Cyp1a1 promoter, block BaP-inducible gene expression and stimulate the formation of BPDE-DNA ..
  34. FOXP3-microRNA146-NFkB Axis in Tumor Suppression
    Lizhong Wang; Fiscal Year: 2013
    ..The potential role in FOXP3-mediated regulation on noncoding RNA has not been studied...
  35. Chronic Stress and Abdominal Pain: Novel Mechanisms
    John W Wiley; Fiscal Year: 2013
    ..to the changes observed in CB and TRP pathways will be confirmed using targeted delivery of gene silencing (si-RNA) reagents in situ and correlation of these interventions with behavior, e.g...
  36. Roles for microRNA-122 in hepatitis C virus RNA amplification
    Peter Sarnow; Fiscal Year: 2013
    ..LNAs) that can easily be delivered to the liver in animals where it sequesters miR-122 in an inactive small duplex RNA. In particular, the first aim will characterize the RNA-RNA interactions in the miR-122/HCV complex, using genetic ..
  37. Epigenomic Events in Development of the Locus Coeruleus Noradrenergic Neurons
    Jan Krzysztof Blusztajn; Fiscal Year: 2012
    ..characterization of the genome-wide developmental pattern of the LCNN transcriptome [for both messenger RNA (mRNA) and microRNA (miRNA)], the DNA CpG methylome, and genome-wide maps of methylated histone H3 (e.g...
  38. Predictors of Pregnancy Outcome in SLE and APS
    Jane E Salmon; Fiscal Year: 2012
    ..centers, obtained detailed medical and obstetrical information monthly, and serially collected plasma, serum, DNA, RNA, and urine...
  39. Overcoming Temozolomide Resistance using MGMT-targeting Spherical Nucleic Acids
    TIMOTHY L SITA; Fiscal Year: 2013
    ..We will utilize small interfering RNA (siRNA) duplexes densely conjugated to the surface of gold nanoparticles (MGMTi-Spherical Nucleic Acids (SNAs))...
  40. Inhibiting Mucosal HIV-1 Transmission by Host Cell RNA Interference
    Alexandra L Howell; Fiscal Year: 2013
    ..We propose to use RNA interference (RNAi) with short-interfering RNA (siRNA) to silence expression of CCR5 and DC-SIGN on mucosal ..
  41. Cellular and Animal Models of FUS Mutations in ALS
    Eric J Huang; Fiscal Year: 2013
    ..These results lead us to hypothesize that mutant FUS proteins dominantly inhibit normal RNA and protein synthesis and thereby suppressing neuronal functions and survival...
  42. Novel genomic effects of Y-linked polymorphisms
    Daniel L Hartl; Fiscal Year: 2012
    ..regulatory pathways associated with position-effect variegation (PEV) and/or repeat- associated small interfering RNA (rasiRNA)...
  43. Functional characters of non-coding RNAs in alcoholic liver injury
    Fanyin Meng; Fiscal Year: 2013
    ..The field of non-coding RNA (ncRNA) molecules represents a paradigm shift in biology, away from the central dogma of biology which places RNA ..
  44. Non-coding RNA engineers antibody diversity
    Uttiya Basu; Fiscal Year: 2011
    ..Approach: WE have previously observed that component of the ncRNA-processing pathway, the RNA exosome complex, regulate CSR in ex vivo assays...
  45. Stem Cell Homing for Treatment of Female Pelvic Floor Disorders
    Margot S Damaser; Fiscal Year: 2013
    ..infusion of MSCs in which homing cytokine receptors have been knocked down via transfection with small interfering RNA (siRNA)...
  46. Interaction between RNA interference and RNA editing pathways
    Kazuko Nishikura; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): One type of RNA editing involves the conversion of adenosine residues into inosine in double-stranded RNA (dsRNA) through the action of adenosine deaminase acting on RNA (ADAR)...
  47. Regulation of NFkappaB activity by the Estrogen Receptor
    Kendall W Nettles; Fiscal Year: 2012
    ..to the MCP-1, IL-6, IL-8, MIP-1 and TNF-a genes by chromatin immunoprecipitation, and assay the effects of RNA interference targeting CBP and Grip1 on expression of the same genes...
    Stephen J Lippard; Fiscal Year: 2013
    ..Because cisplatin blocks RNA polymerase II, which triggers apoptosis and initiates nucleotide excision repair, transcription inhibition by Pt-..
    Michael R Green; Fiscal Year: 2013
    ..Transcription initiation by RNA polymerase II involves the assembly of general transcription factors on the core promoter to form a preinitiation ..
  50. Potential Mechanisms of Glucagon-like peptide-1 in Fatty Liver Disease
    Frank A Anania; Fiscal Year: 2010
    ..Specific Aim 2: To employ RNA interference for GLP-1 receptor and determine whether the gene profile associated with GLP-1, which favors ..
  51. Molecular Biology of Human Erythrocyte Alpha Spectrin
    Patrick G Gallagher; Fiscal Year: 2013
    ..Integration of mRNA transcript composition, genomic organization, RNA polymerase II binding, transcription factor and regulatory protein binding, and histone architecture will provide ..
  52. The Role of Astrocytes in Cortical Interneuron Development
    KAREN MULLER SMITH; Fiscal Year: 2013
    ..affinity purification (TRAP) method, and target validation experiments using in vivo electroporation of silencing RNA (siRNA) constructs...
  53. Knockdown of Gene Expression in Immune Cells in Humanized Mice
    Judy Lieberman; Fiscal Year: 2010
    ..Two recent technologies, RNA interference (RNAi) and humanized mice with robust functional human immune responses, now provide an opportunity ..
  54. Improving Epigenetic-based Cell Reprogramming with Proteasome Inhibition
    Jaroslaw Staszkiewicz; Fiscal Year: 2011
    ..DNA * methyltransferases and histone deacetylases) using interfering RNA technology;3) modulating epigenetic * regulatory components with small molecules;and 4) Combining over-expression ..
  55. Anti-Bacterial Innate Responses Enhance Paramyxovirus Replication
    Griffith D Parks; Fiscal Year: 2010
    ..The central hypotheses to be tested here are that bacterially-derived TLR agonists enhance RNA virus replication through i) activation of cell survival/proliferation pathways, or ii) suppression of antiviral ..
  56. Mechanisms of Angiogenesis in Retinopathy of Prematurity
    Mary Elizabeth Hartnett; Fiscal Year: 2009
    ..cells; laser capture microdissection;real-time-PCR to quantitate and in situ hybridization to detect location of RNA of VEGF isoforms, VEGF receptors 1 and 2, neuropilins;ELISA and Western blot to measure protein (VEGF; cleaved ..
  57. Histone Chaperones in Angiogenesis
    Soumen Paul; Fiscal Year: 2012
    ..Intriguingly, knockdown of HIRA by RNA interference (RNAi) in endothelial cells inhibits angiogenic signal-induced induction of Vegfr1 and other ..
    Vivian Bellofatto; Fiscal Year: 2010
    ..For example, Trypanosoma brucei and other members of the trypanosomatid family contain an unusual RNA polymerase II enzyme and what appears to be an abridged set of transcription factors...
  59. DNA Damage Checkpoint and Cancer
    Toru Ouchi; Fiscal Year: 2012
    ..with other DNA damage-sensing proteins, and whether cell specific-disruption of the BAAT1 pathway using RNA gene targeting approaches facilitates tumor development by genetic and environmental lesions or alters the response ..
  60. Roles of RNA Polymerases IV and V in siRNA-mediated gene silencing
    CRAIG STUART PIKAARD; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): All eukaryotes use three essential DNA-dependent RNA polymerases to decode the genetic information in chromosomal DNA, namely RNA Polymerases I, II and III...
  61. Genetic &Functional Analyses of Hypertension Susceptibility Genes
    YEN PEI CHRISTY CHANG; Fiscal Year: 2013
    ..Therefore we will generate cortex- and medulla-enriched human and mouse kidney transcriptomes by RNA sequencing, which is suitable for the detection of novel isoforms and rare transcripts...
    ELIZABETH ANN LEIBOLD; Fiscal Year: 2013
    ..In vertebrates, iron metabolism is controlled by iron-regulatory protein 2 (IRP2). IRP2 is a RNA-binding protein that binds to iron-responsive elements (IREs) located in mRNAs of proteins involved in iron uptake, ..
  63. Analysis of epigenetic regulation in early mammalian embryos via RNA interference
    Charles R Long; Fiscal Year: 2010
    ..We will test our hypothesis by using RNA interference to study the functional genomics of epigenetic reprogramming in an established model of in vitro ..
  64. Novel CTD inhibitors with synthetic lethality to oncogenic Ras for cancer therapy
    Bingliang Fang; Fiscal Year: 2013
    ..60, or -231 led to suppression of the phosphorylation of the C-terminal domain (CTD) of the largest subunit of RNA polymerase II, whish is consistent with previous reports that the continuous activity of RNA polymerase II is ..
  65. Functional role of a host metabolic enzyme in viral replication
    Peter Nagy; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): Plus-stranded (+)RNA viruses infect all kind of species and cause many serious diseases in humans, animals and plants, leading to major losses in food production and representing significant risk to ..
  66. Host factors involved in viral RNA recombination
    Peter Nagy; Fiscal Year: 2006
    The host plays a role not only in replication of plus-stranded RNA viruses, but also in viral RNA recombination, although the role(s) of host factors in recombination is currently unknown...
  67. The Role of RNA Splicing Factors in Retinal Degeneration
    Michael Farkas; Fiscal Year: 2012
    ..in many genes have been implicated in the disease, we propose to investigate how mutations in genes required for RNA splicing cause dominant RP...
  68. The role of the host Ca/Mn pump in emergence of novel viral RNA recombinants
    Peter Nagy; Fiscal Year: 2010
    ..Evolution of plus- stranded RNA viruses is frequently driven by RNA recombination, a process that joins noncontiguous RNA segments together, ..
  69. Nonstructural roles of capsid proteins in virus replication
    TERYL FREY; Fiscal Year: 2009
    ..RUBV is a simple, plus-strand RNA virus (rubivirus genus, Togavirus family) that has five genes: two replicase genes and three structural protein ..
  70. SRP RNA level as a determinant of leishmanial parasitism of macrophages
    Gautam Chaudhuri; Fiscal Year: 2009
    ..Gene transcripts that are down regulated in macrophages upon exposure to Leishmania include 7SL RNA, the RNA component of the signal recognition particle (SRP)...
    Gaetano Montelione; Fiscal Year: 2000
    ..structure analysis by NMR and to expand our understanding of the details of molecular recognition in protein: RNA complexes...
  72. A novel assay for inhibitors of influenza A virus polymerase complex assembly
    Feng Li; Fiscal Year: 2009
    ..One such target for anti-influenza drug development is the assembly of the viral RNA polymerase complex...
    Terry W Osborn; Fiscal Year: 2010
    ..We have shown, in NC, 20% of the RNA transcripts measured on Affymetrix exon array were not significantly changed over nine consecutive blood draws time ..
  74. Evaluation of RNA transport elements in HIV-1 vectors
    SRINIVAS KUMAR; Fiscal Year: 2007
    DESCRIPTION (provided by applicant): Post-transcriptional regulatory elements (PTREs) effect various aspects of RNA function: transport of RNAs from the nucleus to the cytoplasm, localization of the RNA in specific cellular compartments,..
  75. Role of an essential RNA chaperone in virus replication
    Peter Nagy; Fiscal Year: 2006
    b>RNA replication is the central step in the infection cycles of plus-strand RNA viruses, which cause many diseases in humans, animals and plants...
    SHERRILL ADAMS; Fiscal Year: 1993
    ..However, a unique, previously undescribed RNA species has been detected in chick cartilage...
  77. High-Throughput Identification of RNA polymerase inhibitors in vivo
    Robert Landick; Fiscal Year: 2006
    Bacterial RNA polymerase is both a central target in mechanistic studies of gene regulation and a highly attractive target for new antibiotic development...
    Vitaly Citovsky; Fiscal Year: 2002
    ..studied plant viruses, is mediated by its movement protein (MP), proposed to form complexes with the genomic TMV RNA and target them to and through plant intercellular connections, the plasmodesmata...
  79. Regulation of Sindbis Virus Subgenomic RNA Synthesis
    Victor Stollar; Fiscal Year: 2010
    Sindbis virus, (SV) one of the simplest, enveloped RNA viruses, is the prototype virus of the family Togaviridae, genus alphavirus. It is transmitted to its vertebrate hosts by mosquitoes...
  80. An HBV polymerase RNA binding assay suitable for inhibitor screening
    Feng Cao; Fiscal Year: 2009
    ..Duck Hepatitis B virus (DHBV) reverse transcriptase that together form the site where the enzyme first binds to the RNA form of the viral genome. Disrupting RNA binding at the T3:RT1 site blocks reverse transcription...
    Neerja Kaushik Basu; Fiscal Year: 2006
    Replication of positive stranded RNA viruses in virus-infected cells is believed to be catalyzed by viral replicase complexes, which may consist of various virally encoded nonstructural proteins including the RNA dependent RNA ..
  82. Cis-acting RNA elements in hepatitis C virus replication
    Guangxiang Luo; Fiscal Year: 2007
    ..S. HCV has a positive-stranded RNA genome consisting of a single open reading frame (ORF) flanked by the untranslated regions (UTR) at the 5' and ..