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. 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 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Detail Information

Publications321 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 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...
  3. 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...
  4. 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...
  5. 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...
  6. 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 ..
  7. 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...
  8. 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 ..
  9. 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...
  10. 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...
  11. 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...
  12. 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)...
  13. 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
    ....
  14. 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 ..
  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. ncbi 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...
  17. 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...
  18. 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...
  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 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...
  21. pmc RNA and disease
    Thomas A Cooper
    Department of Pathology, Baylor College of Medicine, Houston, TX 77030, USA
    Cell 136:777-93. 2009
    Cellular functions depend on numerous protein-coding and noncoding RNAs and the RNA-binding proteins associated with them, which form ribonucleoprotein complexes (RNPs)...
  22. 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)...
  23. 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...
  24. ncbi Identification of novel genes coding for small expressed RNAs
    M Lagos-Quintana
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, , Germany
    Science 294:853-8. 2001
    ..This suggests that sequence-specific, posttranscriptional regulatory mechanisms mediated by small RNAs are more general than previously appreciated...
  25. 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...
  26. 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 ..
  27. 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...
  28. 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.
  29. 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...
  30. ncbi 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...
  31. 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...
  32. 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...
  33. 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...
  34. 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...
  35. 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 ..
  36. 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...
  37. pmc T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
    Paolo Di Tommaso
    Centre For Genomic Regulation Pompeu Fabra University, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain
    Nucleic Acids Res 39:W13-7. 2011
    ..available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using ..
  38. 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...
  39. 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...
  40. 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)...
  41. 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...
  42. 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...
  43. 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...
  44. 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...
  45. 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.
  46. 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 ..
  47. 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...
  48. 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...
  49. ncbi 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...
  50. 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...
  51. 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...
  52. 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...
  53. 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...
  54. 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)...
  55. ncbi 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...
  56. 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...
  57. 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...
  58. 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...
  59. ncbi 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...
  60. 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...
  61. 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...
  62. 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...
  63. 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...
  64. 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 ..
  65. 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...
  66. 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...
  67. 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...
  68. pmc Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination
    Konstantina Skourti-Stathaki
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
    Mol Cell 42:794-805. 2011
    We present a molecular dissection of pause site-dependent transcriptional termination for mammalian RNA polymerase II (Pol II)-transcribed genes...
  69. 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...
  70. 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-..
  71. 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...
  72. ncbi 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...
  73. 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 ..
  74. 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...
  75. ncbi 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...
  76. 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...
  77. 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
    ....
  78. 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...
  79. pmc Genomewide RNA expression profiling in lung identifies distinct signatures in idiopathic pulmonary arterial hypertension and secondary pulmonary hypertension
    Revathi Rajkumar
    Cardiovascular Institute, Univ of Pittsburgh, PA 15213 2582, USA
    Am J Physiol Heart Circ Physiol 298:H1235-48. 2010
    ..Using genomewide microarray analysis, we generated the largest data set to date of RNA expression profiles from lung tissue specimens from 1) 18 PAH subjects and 2) 8 subjects with PH secondary to ..
  80. pmc Role of RNA structure in regulating pre-mRNA splicing
    M Bryan Warf
    Institute of Molecular Biology, and Department of Chemistry, University of Oregon, Eugene, Oregon 97403, USA
    Trends Biochem Sci 35:169-78. 2010
    Pre-mRNA splicing involves removing non-coding introns from RNA transcripts. It is carried out by the spliceosome, along with other auxiliary factors...
  81. pmc Chronic inflammation in fat plays a crucial role in the development of obesity-related insulin resistance
    Haiyan Xu
    Millennium Pharmaceuticals, Cambridge, Massachusetts, USA
    J Clin Invest 112:1821-30. 2003
    ..We propose that obesity-related insulin resistance is, at least in part, a chronic inflammatory disease initiated in adipose tissue...
  82. ncbi 5'-Triphosphate RNA is the ligand for RIG-I
    Veit Hornung
    Division of Clinical Pharmacology, Department of Internal Medicine, University of Munich, 80336 Munich, Germany
    Science 314:994-7. 2006
    The structural basis for the distinction of viral RNA from abundant self RNA in the cytoplasm of virally infected cells is largely unknown...
  83. pmc RNA toxicity is a component of ataxin-3 degeneration in Drosophila
    Ling Bo Li
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 6018, USA
    Nature 453:1107-11. 2008
    ..Here we provide evidence for a pathogenic role of the CAG repeat RNA in polyQ toxicity using Drosophila...
  84. ncbi Characterization and functional implications of the RNA binding properties of nuclear factor TDP-43, a novel splicing regulator of CFTR exon 9
    E Buratti
    International Center for Genetic Engineering and Biotechnology ICGEB 34012 Trieste, Italy
    J Biol Chem 276:36337-43. 2001
    ..In this study we report the dissection of the RNA binding properties of TDP-43 and their functional implications in relationship with the splicing process...
  85. 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...
  86. pmc FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing
    Jason G Underwood
    Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA
    Nat Methods 7:995-1001. 2010
    Classical approaches to determine structures of noncoding RNA (ncRNA) probed only one RNA at a time with enzymes and chemicals, using gel electrophoresis to identify reactive positions...
  87. pmc RNA-based gene duplication: mechanistic and evolutionary insights
    Henrik Kaessmann
    Center for Integrative Genomics, University of Lausanne, Genopode, CH 1015 Lausanne, Switzerland
    Nat Rev Genet 10:19-31. 2009
    ..For example, analyses of chromosomal gene movement patterns via RNA-based gene duplication have shed fresh light on the evolutionary origin and biology of our sex chromosomes.
  88. doi Roles of trinucleotide-repeat RNA in neurological disease and degeneration
    Ling Bo Li
    Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
    Trends Neurosci 33:292-8. 2010
    ..Greater understanding of these mechanisms will provide the foundation for therapeutic advances for this set of human disorders...
  89. doi NMD: RNA biology meets human genetic medicine
    Madhuri Bhuvanagiri
    University of Heidelberg and European Molecular Biology Laboratory, Germany
    Biochem J 430:365-77. 2010
    ....
  90. pmc A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species
    Song Liu
    Department of Biostatistics, Roswell Park Cancer Institute, The State University of New York at Buffalo, Buffalo, NY 14203, USA
    Nucleic Acids Res 39:578-88. 2011
    b>RNA-Seq has emerged as a revolutionary technology for transcriptome analysis...
  91. pmc RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage
    Matthias Schaefer
    Division of Epigenetics, DKFZ ZMBH Alliance, German Cancer Research Center, Heidelberg 69120, Germany
    Genes Dev 24:1590-5. 2010
    ..These results uncover a novel biological function of Dnmt2-mediated tRNA methylation, and suggest a role for Dnmt2 enzymes during the biogenesis of tRNA-derived small RNAs...
  92. pmc Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila
    Sergei Nechaev
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Science 327:335-8. 2010
    Emerging evidence indicates that gene expression in higher organisms is regulated by RNA polymerase II stalling during early transcription elongation...
  93. pmc Self-RNA-antimicrobial peptide complexes activate human dendritic cells through TLR7 and TLR8
    Dipyaman Ganguly
    Department of Immunology, The University of Texas M D Anderson Cancer Center, TX 77030, USA
    J Exp Med 206:1983-94. 2009
    Dendritic cell (DC) responses to extracellular self-DNA and self-RNA are prevented by the endosomal seclusion of nucleic acid-recognizing Toll-like receptors (TLRs)...
  94. pmc Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs
    Rui Yi
    Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
    Genes Dev 17:3011-6. 2003
    ..initially expressed as long transcripts that are processed in the nucleus to yield approximately 65-nucleotide (nt) RNA hairpin intermediates, termed pre-miRNAs, that are exported to the cytoplasm for additional processing to yield ..
  95. ncbi Leptin levels in human and rodent: measurement of plasma leptin and ob RNA in obese and weight-reduced subjects
    M Maffei
    Laboratory of Molecular Genetics, Rockefeller University, New York, New York 10021, USA
    Nat Med 1:1155-61. 1995
    ..Weight loss due to food restriction was associated with a decrease in plasma leptin in samples from mice and obese humans...
  96. doi RNA granules: post-transcriptional and epigenetic modulators of gene expression
    Paul Anderson
    Division of Rheumatology, Immunology and Allergy, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Rev Mol Cell Biol 10:430-6. 2009
    ..The protein components of selected mRNP complexes promote their assembly into microscopically visible cytoplasmic RNA granules, including stress granules, processing bodies and germ cell (or polar) granules...
  97. ncbi Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis
    Claire L Wilson
    Paterson Institute for Cancer Research, Manchester M20 4BX, UK
    Bioinformatics 21:3683-5. 2005
    ..Simpleaffy is a BioConductor package that provides access to a variety of QC metrics for assessing the quality of RNA samples and of the intermediate stages of sample preparation and hybridization...
  98. pmc Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing
    Chryssa Kanellopoulou
    The Dana Farber Cancer Institute, Department of Cancer Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genes Dev 19:489-501. 2005
    Dicer is the enzyme that cleaves double-stranded RNA (dsRNA) into 21-25-nt-long species responsible for sequence-specific RNA-induced gene silencing at the transcriptional, post-transcriptional, or translational level...
  99. pmc Computational approaches for RNA energy parameter estimation
    Mirela Andronescu
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    RNA 16:2304-18. 2010
    Methods for efficient and accurate prediction of RNA structure are increasingly valuable, given the current rapid advances in understanding the diverse functions of RNA molecules in the cell...
  100. ncbi PSF and p54(nrb)/NonO--multi-functional nuclear proteins
    Yaron Shav-Tal
    Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
    FEBS Lett 531:109-14. 2002
    ....
  101. ncbi RNA-targeted splice-correction therapy for neuromuscular disease
    Matthew J A Wood
    Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
    Brain 133:957-72. 2010
    Splice-modulation therapy, whereby molecular manipulation of premessenger RNA splicing is engineered to yield genetic correction, is a promising novel therapy for genetic diseases of muscle and nerve-the prototypical example being ..

Research Grants140 found, 100 shown here

  1. CONTROL OF CELL FUNCTION VIA SELECTIVE MRNA TRANSLATION
    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. Bioengineering Core for Cellular and Tissue Models
    Andrew McCulloch; Fiscal Year: 2009
    ..1996). The cells are serum-depleted for 24 hr followed by passive stretch for an additional 24 hr. Total RNA is extracted and subjected to RNA protection assay (RPA) using Direct RPA system (Ambion Inc.)...
  3. 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 ..
  4. 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. ..
  5. Biomedical Simulations Resource (BMSR)
    DAVID Z D apos ARGENIO; Fiscal Year: 2010
    ..in 1 Examples of in vitro evolution methods include aptamer selection, SELEX, phage display, polyribosome display, RNA display and peptides on plasmids...
  6. A Network Biology Approach to Antibiotic Action and Bacterial Defense Mechanisms
    James Collins; Fiscal Year: 2009
    ..This project may thus enable the development of novel classes of antibiotics that account for and utilize the complex regulatory properties of genetic networks. ..
  7. Molecular Biology Core Laboratory
    David Russell; Fiscal Year: 2009
    ..hybridization and real-time polymerase chain reactions (PCRs), oligonucleotide procurement, genomic DMA and RNA isolation, and the maintenance and storage of bacterial strains, plasmids, and purified proteins used within this ..
  8. Regulation of HSV-1 Gene Expression and Replication by Nuclear Hormone Receptors
    SHAOCHUNG VICTOR HSIA; Fiscal Year: 2012
    ..RCC1/Ran complex is involved in the control of RNA translocation, DNA synthesis, and cell cycle progression via modulating effects on chromatin and nucleosomes...
  9. 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...
  10. 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...
  11. Cardiotrophin-Like Cytokine 1, a Candidate Molecule for the FSGS Factor
    Virginia J Savin; Fiscal Year: 2009
    ..Preliminary studies show that anti-CLC-1 blocks the effect of FSGS serum and that glomeruli express RNA for receptor components...
  12. 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...
  13. 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 ..
  14. 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 ..
  15. Lung Lysyl Oxidase Regulation by Metal Ion Homeostasis
    Wande Li; Fiscal Year: 2010
    ..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 ..
  16. 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 ..
  17. 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...
  18. 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...
  19. Discovery of Small Molecule MBT Domain Antagonists
    STEPHEN FRYE; Fiscal Year: 2009
    ..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...
  20. 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...
  21. 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 ..
  22. 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...
  23. 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 ..
  24. Targeted siRNA nanotechnology for intravesical treatment of urologicaldiseases
    Robert Weiss; Fiscal Year: 2009
    ..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 ..
  25. 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,..
  26. 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,..
  27. REGULATION OF ATROPHY-INDUCED PROGENITOR CELLS IN THE GASTRIC CORPUS
    Jason C Mills; Fiscal Year: 2012
    ..CD44-expressing epithelial progenitor cells by FACS and laser-capture microdissection and then use RNA-Seq to generate gene expression profiles of the normal and atrophy-expanded progenitor cells that will then be ..
  28. Viral and Bacterial DNA Ligases
    STEWART H SHUMAN; Fiscal Year: 2010
    ..b>RNA ligases participate in breakage-repair pathways that underlie tRNA splicing, post-transcriptional RNA editing, and ..
  29. DNA SEQUENCES IMPACT ESTROGEN AND ANTIESTROGEN ACTIVITY
    Carolyn M Klinge; Fiscal Year: 2010
    ..ChIP assays will determine if E2 increases the direct interaction of ER1, coactivators, and RNA pol II with the NRF-1 promoter in vivo in MCF-7 tumor xenografts and mouse tissues, focusing first on uterus...
  30. DNA SEQUENCES IMPACT ESTROGEN AND ANTIESTROGEN ACTIVITY
    CAROLYN KLINGE; Fiscal Year: 2009
    ..ChIP assays will determine if E2 increases the direct interaction of ER1, coactivators, and RNA pol II with the NRF-1 promoter in vivo in MCF-7 tumor xenografts and mouse tissues, focusing first on uterus...
  31. DNA SEQUENCES IMPACT ESTROGEN AND ANTIESTROGEN ACTIVITY
    Carolyn M Klinge; Fiscal Year: 2010
    ..ChIP assays will determine if E2 increases the direct interaction of ER1, coactivators, and RNA pol II with the NRF-1 promoter in vivo in MCF-7 tumor xenografts and mouse tissues, focusing first on uterus...
  32. MOLECULAR BASIS OF REOVIRUS PATHOGENESIS
    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...
  33. MOLECULAR BASIS OF REOVIRUS PATHOGENESIS
    Terence S Dermody; Fiscal Year: 2011
    ..a fully plasmid-based reverse genetics system for reovirus, the first of its kind for any mammalian double-stranded RNA virus...
  34. 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 ..
  35. Trichothecene Toxicity and the Ribotoxic Stress Response
    James J Pestka; Fiscal Year: 2010
    ..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 ..
  36. Trichothecene Toxicity and the Ribotoxic Stress Response
    James J Pestka; Fiscal Year: 2010
    ..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 ..
  37. Vitamin D and Estrogen Action in Bone: Concerted Role for hnRNPs in the C Family
    John S Adams; Fiscal Year: 2011
    ..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 ..
  38. Vitamin D and Estrogen Action in Bone: Concerted Role for hnRNPs in the C Family
    John S Adams; Fiscal Year: 2010
    ..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 ..
  39. 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...
  40. Reactivation of Fetal Gamma-globin Genes for the Treatment of Beta-globin Disorde
    JAMES ENGEL; Fiscal Year: 2009
    ..The first will be to develop highly efficient small interfering RNA (siRNA) duplexes that specifically knock-down TR2, TR4, or their potential co-regulatory proteins by RNA ..
  41. Steroid Responsive Mechanisms in the Ear
    DENNIS ROYAL TRUNE; Fiscal Year: 2010
    ..with ELISA, and 5) steroid-mediated cochlear gene products will be assessed with ELISA, Western blot, cytokine RNA expression, and quantitative RT-PCR...
  42. Steroid Responsive Mechanisms in the Ear
    Dennis Trune; Fiscal Year: 2009
    ..with ELISA, and 5) steroid-mediated cochlear gene products will be assessed with ELISA, Western blot, cytokine RNA expression, and quantitative RT-PCR...
  43. 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 ..
  44. BIOCHEMISTRY OF PRE-MRNA SPLICING
    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...
  45. MECHANISM OF LATENCY OF HERPES SIMPLEX VIRUS
    Donald Coen; Fiscal Year: 2009
    ..structure of additional LAT gene mutant viruses, by determining if the LAT gene effects on chromatin are due to RNA silencing or X inactivation mechanisms, by determining if the HSV immediate early ICPO protein affects viral ..
  46. 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...
  47. Mitochondrial dysfunction, oxidative stress, and surgical acute kidney injury
    FREDERIC TREMAINE BILLINGS; Fiscal Year: 2013
    ..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 (..
  48. 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 ..
  49. Functional role of a host metabolic enzyme in viral replication
    Peter Nagy; Fiscal Year: 2009
    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 ..
  50. The Role of RNA Splicing Factors in Retinal Degeneration
    Michael Farkas; Fiscal Year: 2010
    ..in many genes have been implicated in the disease, we propose to investigate how mutations in genes required for RNA splicing cause dominant RP...
  51. 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...
  52. Host factors involved in viral RNA recombination
    Peter Nagy; Fiscal Year: 2005
    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...
  53. 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...
  54. Ty3 viruslike particle morphogenesis and host interactions
    Suzanne Sandmeyer; Fiscal Year: 2010
    ..In the current funding period, the assembling Ty3 VLP was characterized by density sedimentation, RNA protection, transmission EM and atomic force microscopy performed on Ty3 VLPs blocked at specific stages and also ..
  55. 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, ..
  56. The role of the host Ca/Mn pump in emergence of novel viral RNA recombinants
    Peter Nagy; Fiscal Year: 2009
    ..Evolution of plus- stranded RNA viruses is frequently driven by RNA recombination, a process that joins noncontiguous RNA segments together, ..
  57. 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 ..
  58. The influenza A virus nucleoprotein: structure and function
    YIZHI JANE contact TAO; Fiscal Year: 2010
    ..The genome of influenza A virus consists of eight segments of (-)RNA that are encapsidated in distinct double-helical structures called the ribonucleoprotein (RNP) complexes...
  59. The influenza A virus nucleoprotein: structure and function
    Yizhi Tao; Fiscal Year: 2009
    ..The genome of influenza A virus consists of eight segments of (-)RNA that are encapsidated in distinct double-helical structures called the ribonucleoprotein (RNP) complexes...
  60. Viral and Bacterial DNA Ligases
    Stewart Shuman; Fiscal Year: 2009
    ..b>RNA ligases participate in breakage-repair pathways that underlie tRNA splicing, post-transcriptional RNA editing, and ..
  61. CONTROL OF CELL FUNCTION VIA SELECTIVE MRNA TRANSLATION
    Lee Gehrke; Fiscal Year: 2000
    ..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...
  62. CONTROL OF CELL FUNCTION VIA SELECTIVE MRNA TRANSLATION
    Lee Gehrke; Fiscal Year: 2001
    ..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...
  63. CONTROL OF CELL FUNCTION VIA SELECTIVE MRNA TRANSLATION
    Lee Gehrke; Fiscal Year: 1999
    ..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...
  64. 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)...
  65. STRUCTURES OF RNA BINDING PROTEINS FROM INFLUENZA VIRUS
    Gaetano Montelione; Fiscal Year: 1999
    ..structure analysis by NMR and to expand our understanding of the details of molecular recognition in protein: RNA complexes...
  66. STRUCTURES OF RNA BINDING PROTEINS FROM INFLUENZA VIRUS
    Gaetano Montelione; Fiscal Year: 2000
    ..structure analysis by NMR and to expand our understanding of the details of molecular recognition in protein: RNA complexes...
  67. EXPRESSION OF SNRNA GENES
    Nouria Hernandez; Fiscal Year: 1993
    In eucaryotes, transcription is carried out by three evolutionary related RNA polymerases, each of which recognizes a different type of promoter...
  68. EXPRESSION OF SNRNA GENES
    Nouria Hernandez; Fiscal Year: 1992
    In eucaryotes, transcription is carried out by three evolutionary related RNA polymerases, each of which recognizes a different type of promoter...
  69. True Direct Single Molecule RNA Sequencing
    PATRICE MARIE MILOS; Fiscal Year: 2010
    ..Current methods, however, typically require RNA to be converted to cDNA prior to measurements. This step has been shown to introduce many biases and artifacts...
  70. 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...
  71. Involvement of Proteins in Splicing Group I and Group II Introns
    Alan Lambowitz; Fiscal Year: 2007
    ..These introns use RNA-catalyzed splicing mechanisms, but require proteins to help fold the intron RNA into the catalyti- cally active ..
  72. Involvement of Proteins in Splicing Group I and Group II Introns
    Alan Lambowitz; Fiscal Year: 2009
    ..These introns use RNA-catalyzed splicing mechanisms, but require proteins to help fold the intron RNA into the catalyti- cally active ..
  73. Involvement of Proteins in Splicing Group I and Group II Introns
    Alan M Lambowitz; Fiscal Year: 2010
    ..These introns use RNA-catalyzed splicing mechanisms, but require proteins to help fold the intron RNA into the catalyti- cally active ..
  74. 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...
  75. Involvement of Proteins in Splicing Group I and Group II Introns
    Alan Lambowitz; Fiscal Year: 2009
    ..These introns use RNA-catalyzed splicing mechanisms, but require proteins to help fold the intrpn RNA into the catalyti- cally active ..
  76. X-ray crystallographic studies of multi-subunit nucleic acid polymerases
    Katsuhiko Murakami; Fiscal Year: 2010
    The goal of this proposal is to determine the X-ray crystal structures of archaeal RNA polymerase and its complexes with auxiliary protein factors and nucleic acid...
  77. X-ray crystallographic studies of multi-subunit nucleic acid polymerases
    Katsuhiko Murakami; Fiscal Year: 2010
    The goal of this proposal is to determine the X-ray crystal structures of archaeal RNA polymerase and its complexes with auxiliary protein factors and nucleic acid...
  78. GENE EXPRESSION EXON ARRAY BIOMARKERS TO DIAGNOSE SCHIZOPHRENIA
    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 ..
  79. Structural Studies of RNA Maturation and Processing
    Christopher D Lima; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): The function and stability of eukaryotic RNA is regulated by co- and post-transcriptional modifications that include mRNA capping, splicing, and polyadenylation as well as processing and ..
  80. Evaluation of RNA transport elements in HIV-1 vectors
    SRINIVAS KUMAR; Fiscal Year: 2004
    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, association with ribosomes, and ..
  81. 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,..
  82. Evaluation of RNA transport elemeents in HIV-1 vectors
    SRINIVAS KUMAR; Fiscal Year: 2005
    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, association with ribosomes, and ..
  83. Evaluation of RNA transport elemeents in HIV-1 vectors
    SRINIVAS KUMAR; Fiscal Year: 2006
    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,..
  84. Role of an essential RNA chaperone in virus replication
    Peter Nagy; Fiscal Year: 2005
    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...
  85. 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...