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. ncbi 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. ncbi 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
  3. ncbi 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
  4. ncbi 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
  5. ncbi 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
  6. ncbi 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
  7. ncbi Infernal 1.0: inference of RNA alignments
    Eric P Nawrocki
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Bioinformatics 25:1335-7. 2009
  8. ncbi 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
  9. ncbi 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. ncbi 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

Research Grants

  1. CONTROL OF CELL FUNCTION VIA SELECTIVE MRNA TRANSLATION
    Lee Gehrke; Fiscal Year: 2002
  2. Development of tools for structural genomics of viral RNA
    JEFFREY KIEFT; Fiscal Year: 2007
  3. Host factors involved in viral RNA recombination
    Peter Nagy; Fiscal Year: 2006
  4. Ty3 viruslike particle morphogenesis and host interactions
    Suzanne Sandmeyer; Fiscal Year: 2010
  5. The influenza A virus nucleoprotein: structure and function
    YIZHI JANE contact TAO; Fiscal Year: 2010
  6. The influenza A virus nucleoprotein: structure and function
    Yizhi Tao; Fiscal Year: 2009
  7. Viral and Bacterial DNA Ligases
    STEWART H SHUMAN; Fiscal Year: 2010
  8. Viral and Bacterial DNA Ligases
    Stewart Shuman; Fiscal Year: 2009
  9. Structural Studies of RNA Maturation and Processing
    Christopher D Lima; Fiscal Year: 2010
  10. EXPRESSION OF SNRNA GENES
    Nouria Hernandez; Fiscal Year: 1993

Detail Information

Publications265 found, 100 shown here

  1. ncbi 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. ncbi 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
    ....
  3. ncbi 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...
  4. ncbi 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)...
  5. ncbi 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...
  6. ncbi 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...
  7. ncbi 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 ..
  8. ncbi 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)...
  9. ncbi 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. ncbi 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...
  11. ncbi 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...
  12. ncbi 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...
  13. ncbi 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)...
  14. ncbi 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...
  15. 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...
  16. 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...
  17. ncbi 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 ..
  18. ncbi 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...
  19. ncbi 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...
  20. ncbi 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...
  21. ncbi 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 ..
  22. ncbi 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...
  23. ncbi 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
    DESCRIPTION: 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...
  24. ncbi 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...
  25. 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...
  26. ncbi 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.
  27. 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 ..
  28. 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
    ....
  29. ncbi 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...
  30. ncbi 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...
  31. ncbi Exploiting structural and topological information to improve prediction of RNA-protein binding sites
    Stefan R Maetschke
    Institute for Molecular Bioscience, University of Queensland, QLD 4072, Australia
    BMC Bioinformatics 10:341. 2009
    b>RNA-protein interactions are important for a wide range of biological processes. Current computational methods to predict interacting residues in RNA-protein interfaces predominately rely on sequence data...
  32. ncbi 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...
  33. ncbi 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...
  34. 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...
  35. ncbi 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...
  36. ncbi 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...
  37. ncbi Structure of PTB bound to RNA: specific binding and implications for splicing regulation
    Florian C Oberstrass
    Institute for Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology, Zurich, ETH Honggerberg, CH 8093 Zurich, Switzerland
    Science 309:2054-7. 2005
    The polypyrimidine tract binding protein (PTB) is a 58-kilodalton RNA binding protein involved in multiple aspects of messenger RNA metabolism, including the repression of alternative exons...
  38. ncbi 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)...
  39. ncbi 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...
  40. ncbi 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...
  41. ncbi 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.
  42. ncbi 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. ncbi A Pumilio-induced RNA structure switch in p27-3' UTR controls miR-221 and miR-222 accessibility
    Martijn Kedde
    Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
    Nat Cell Biol 12:1014-20. 2010
    Key regulators of 3' untranslated regions (3' UTRs) are microRNAs and RNA-binding proteins (RBPs)...
  44. ncbi RNA chaperones, RNA annealers and RNA helicases
    Lukas Rajkowitsch
    Max F Perutz Laboratories, University of Vienna, Vienna, Austria
    RNA Biol 4:118-30. 2007
    b>RNA molecules face difficulties when folding into their native structures...
  45. ncbi Characterization of the RNA content of chromatin
    Tanmoy Mondal
    Department of Genetics and Pathology, Uppsala University, Uppsala S 75185, Sweden
    Genome Res 20:899-907. 2010
    Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure...
  46. ncbi 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...
  47. ncbi DARNED: a DAtabase of RNa EDiting in humans
    Anmol Kiran
    Biochemistry Department, University College Cork, Ireland
    Bioinformatics 26:1772-6. 2010
    b>RNA editing is a phenomenon, which is responsible for the alteration of particular nucleotides in RNA sequences relative to their genomic templates...
  48. ncbi A slow RNA polymerase II affects alternative splicing in vivo
    Manuel De la Mata
    Laboratorio de Fisiologia y Biologia Molecular, Departamento de Fisiologia, Biologia Molecular y Celular, IFIBYNE CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellon 2, Buenos Aires, Argentina
    Mol Cell 12:525-32. 2003
    ..It has been proposed that the promoter effect involves modulation of RNA pol II elongation rates...
  49. ncbi R loops stimulate genetic instability of CTG.CAG repeats
    Yunfu Lin
    Baylor College of Medicine, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, One Baylor Plaza, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 107:692-7. 2010
    ..We demonstrate, using biochemical and genetic approaches, that the formation of stable RNA.DNA hybrids enhances the instability of CTG.CAG repeat tracts...
  50. ncbi Improved RNA secondary structure prediction by maximizing expected pair accuracy
    Zhi John Lu
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
    RNA 15:1805-13. 2009
    Free energy minimization has been the most popular method for RNA secondary structure prediction for decades. It is based on a set of empirical free energy change parameters derived from experiments using a nearest-neighbor model...
  51. ncbi Sequence-non-specific effects of RNA interference triggers and microRNA regulators
    Marta Olejniczak
    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
    Nucleic Acids Res 38:1-16. 2010
    b>RNA reagents of diverse lengths and structures, unmodified or containing various chemical modifications are powerful tools of RNA interference and microRNA technologies...
  52. ncbi RNA molecules stimulate prion protein conversion
    Nathan R Deleault
    Department of Biochemistry, 7200 Vail Building, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
    Nature 425:717-20. 2003
    ..Here we report that stoichiometric transformation of PrP(C) to PrPres in vitro requires specific RNA molecules...
  53. ncbi 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...
  54. ncbi XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure
    C M Clemson
    Department of Cell Biology, University of Massachusetts Medical Center, Worcester 01655, USA
    J Cell Biol 132:259-75. 1996
    The XIST gene is implicated in X chromosome inactivation, yet the RNA contains no apparent open reading frame. An accumulation of XIST RNA is observed near its site of transcription, the inactive X chromosome (Xi)...
  55. ncbi Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations
    Michael W Pfaffl
    Physiology, FML Weihenstephan, Centre of Life and Food Science, Technical University of Munich, Germany
    Biotechnol Lett 26:509-15. 2004
    ..housekeeping genes and 10 members of the somatotropic axis differentially expressed in bovine corpora lutea total RNA. The BestKeeper application and necessary information about data processing and handling can be downloaded on http:/..
  56. ncbi A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing
    Jacob R Borden
    Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
    Metab Eng 12:268-81. 2010
    ..Several corresponding antisense RNA molecules were identified both in 824(pRD7) and 824(pSOS95del), but at much higher levels in 824(pRD7)...
  57. ncbi Computational approaches to 3D modeling of RNA
    Christian Laing
    Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
    J Phys Condens Matter 22:283101. 2010
    Many exciting discoveries have recently revealed the versatility of RNA and its importance in a variety of functions within the cell...
  58. ncbi Competition between the RNA transcript and the nontemplate DNA strand during R-loop formation in vitro: a nick can serve as a strong R-loop initiation site
    Deepankar Roy
    Department of Pathology, USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089 9176, USA
    Mol Cell Biol 30:146-59. 2010
    Upon transcription of some sequences by RNA polymerases in vitro or in vivo, the RNA transcript can thread back onto the template DNA strand, resulting in an R loop...
  59. ncbi A pipeline for RNA-seq data processing and quality assessment
    Angela Goncalves
    EMBL Outstation Hinxton, European Bioinformatics Institute, Cambridge, UK
    Bioinformatics 27:867-9. 2011
    ..expression estimation and data quality assessment of high-throughput sequencing transcriptional profiling (RNA-seq) datasets...
  60. ncbi Gene expression profiling of whole blood: comparison of target preparation methods for accurate and reproducible microarray analysis
    Kristina Vartanian
    Gene Microarray Shared Resource, Oregon Health and Science University, Portland, OR, USA
    BMC Genomics 10:2. 2009
    ..While there can be significant advantages to analyzing RNA isolated from whole blood, particularly in clinical studies, the preparation of samples for microarray analysis is ..
  61. ncbi PNPASE regulates RNA import into mitochondria
    Geng Wang
    Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
    Cell 142:456-67. 2010
    b>RNA import into mammalian mitochondria is considered essential for replication, transcription, and translation of the mitochondrial genome but the pathway(s) and factors that control this import are poorly understood...
  62. ncbi 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...
  63. 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...
  64. ncbi NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
    Douglas H Turner
    Department of Chemistry and Center for RNA Biology, Box 0216, University of Rochester, Rochester, NY 14627 0216, USA
    Nucleic Acids Res 38:D280-2. 2010
    The Nearest Neighbor Database (NNDB, http://rna.urmc.rochester.edu/NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities...
  65. ncbi Analysis of four-way junctions in RNA structures
    Christian Laing
    Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, 10012, USA
    J Mol Biol 390:547-59. 2009
    b>RNA secondary structures can be divided into helical regions composed of canonical Watson-Crick and related base pairs, as well as single-stranded regions such as hairpin loops, internal loops, and junctions...
  66. ncbi Expression of axin2 is regulated by the alternative 5'-untranslated regions of its mRNA
    Thomas A Hughes
    Molecular Haematology and Cancer Biology Unit, Camelia Botnar Laboratories, Institute of Child Health, 30 Guilford St, London WC1N 1EH, United Kingdom
    J Biol Chem 280:8581-8. 2005
    ..We discuss this complex regulation in the context of the function of Axin2 as a tumor suppressor...
  67. ncbi Gene structure of the goldfish agouti-signaling protein: a putative role in the dorsal-ventral pigment pattern of fish
    Jose Miguel Cerdá-Reverter
    Department of Fish Reproductive Physiology, Instituto de Acuicultura de Torre de la Sal, Consejo Superior de Investigaciones Cientificas, 12595 Torre de la Sal, Ribera de Cabanes, Castellon, Spain
    Endocrinology 146:1597-610. 2005
    ..Our studies support agouti signaling protein as the melanization inhibition factor, a key factor in the development of the dorsal-ventral pigment pattern in fish...
  68. ncbi Doublecortin kinase-2, a novel doublecortin-related protein kinase associated with terminal segments of axons and dendrites
    Arthur M Edelman
    Department of Pharmacology and Toxicology, State University of New York, Buffalo, New York 14214, USA
    J Biol Chem 280:8531-43. 2005
    ..DCK2 may represent a phosphorylation-dependent switch for the reversible control of MT dynamics in the vicinity of neuronal growth cones...
  69. ncbi Tissue-specific translation of murine branched-chain alpha-ketoacid dehydrogenase kinase mRNA is dependent upon an upstream open reading frame in the 5'-untranslated region
    Eric A Muller
    Graduate Program in Genetics and Molecular Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
    J Biol Chem 279:44645-55. 2004
    ..The location and putative 19-residue peptide are conserved in the mouse, rat, chimpanzee, and human genes. Likewise, gene structure of mouse, chimpanzee, and human BCKD-kinase is conserved, whereas the rat gene has lost intron 9...
  70. ncbi Molecular cloning, expression and characterization of cDNAs encoding the ferritin subunits from the beetle, Apriona germari
    Seong Ryul Kim
    College of Natural Resources and Life Science, Dong-A University, 604-714 Busan, South Korea
    Comp Biochem Physiol B Biochem Mol Biol 138:423-33. 2004
    ..Western blot analysis and iron staining assay confirmed that A. germari ferritin has a native molecular mass of approximately 680 kDa...
  71. ncbi Towards a therapeutic inhibition of dystrophin exon 23 splicing in mdx mouse muscle induced by antisense oligoribonucleotides (splicomers): target sequence optimisation using oligonucleotide arrays
    Ian R Graham
    Centre for Biomedical Science, School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
    J Gene Med 6:1149-58. 2004
    ..has been demonstrated in a number of model systems, including constitutively spliced exons in mouse dystrophin RNA. Splicomer reagents directed to Duchenne muscular dystrophy (DMD) RNAs might thus circumvent nonsense or frame-..
  72. ncbi Cloning and identification of hepatocellular carcinoma down-regulated mitochondrial carrier protein, a novel liver-specific uncoupling protein
    Michelle G K Tan
    Department of Clinical Research, Singapore General Hospital, Singapore
    J Biol Chem 279:45235-44. 2004
    ..The down-regulation of HDMCP in HCC cancer cells might result in the elevation of DeltaPsim, a common phenomenon found in cancer cells...
  73. ncbi Foxh1 is essential for development of the anterior heart field
    Ingo Von Both
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
    Dev Cell 7:331-45. 2004
    ..Thus, Foxh1 and Nkx2-5 functionally interact and are essential for development of the AHF and its derivatives, the RV and OFT, in response to TGFbeta-like signals...
  74. ncbi Circular box C/D RNAs in Pyrococcus furiosus
    Natalia G Starostina
    Department of Biochemistry and Molecular Biology, University of Georgia, Davison Life Science Building, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 101:14097-101. 2004
    Box C/D RNAs are small, noncoding RNAs that function in RNA modification in eukaryotes and archaea. Here, we report that box C/D RNAs exist in the rare biological form of RNA circles in the hyperthermophilic archaeon Pyrococcus furiosus...
  75. ncbi Novel splicing variant of mouse Orc1 is deficient in nuclear translocation and resistant for proteasome-mediated degradation
    Yasuyuki Miyake
    Cellular Physiology Laboratory, RIKEN Discovery Research Institute, Wako, Saitama 351 0198, Japan
    J Biol Chem 280:12643-52. 2005
    ..cDNAs from mouse NIH3T3 cells and found novel variant forms of Orc1, Orc2, and Orc3 each derived from alternative RNA splicing...
  76. ncbi Rad51-related changes in global gene expression
    Lukas M Orre
    Cancer Center Karolinska Institutet, Department of Oncology and Pathology, Division of Medical Radiation Biology, CCK R8 00 Karolinska Institute, SE 171 76 Stockholm, Sweden
    Biochem Biophys Res Commun 341:334-42. 2006
    ....
  77. ncbi Involvement of the mouse Prp19 gene in neuronal/astroglial cell fate decisions
    Yumiko Urano
    Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Yamazaki, Noda shi, Chiba 270 8510, Japan
    J Biol Chem 281:7498-514. 2006
    ..The forced expression of the alpha-variant RNA caused the down-regulation of oct-3/4 and nanog mRNA expression during the 12-48 h of the late-early stages of ..
  78. ncbi Detection of an mRNA polymorphism by differential display
    Shan Liang
    Department of Psychiatry, Vanderbilt University Medical Center, Nashville, TN, USA
    Methods Mol Biol 317:279-85. 2006
    ..Polymorphic transcripts of a single gene differing by one tandem repeat sequence of four nucleotides (TGAT) in the 3' noncoding region were detected...
  79. ncbi Cloning and characterization of a non-TIR-NBS-LRR type disease resistance gene analogue from peach
    Feng-Shan Liang
    Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
    DNA Seq 16:103-10. 2005
    ..The isolation of putative resistance genes from peach provided useful bases for studying the structure and function of peach disease-resistance relating genes and disease resistant genetic breeding in peach...
  80. ncbi Role of upstream stimulatory factor phosphorylation in the regulation of the prostaglandin G/H synthase-2 promoter in granulosa cells
    Khampoune Sayasith
    Centre de Recherche en Reproduction Animale and the Département de Biomédecine Vétérinaire, Faculte de Medecine Veterinaire, Universite de Montreal, Saint Hyacinthe, Quebec J2S 7C6, Canada
    J Biol Chem 280:28885-93. 2005
    ....
  81. ncbi Template switching within exons 3 and 4 of KV11.1 (HERG) gives rise to a 5' truncated cDNA
    S Ro
    Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, 89557, USA
    Biochem Biophys Res Commun 345:1342-9. 2006
    ..The 171 bp deletion was absent at the higher temperature. Our results suggest that the sequence and secondary structure of mRNA in the G/C rich region leads to template switching producing a cDNA product with a 171 bp deletion...
  82. ncbi Molecular cloning and expression of Ad4BP/SF-1 in the serial sex changing gobiid fish, Trimma okinawae
    Yasuhisa Kobayashi
    Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu cho, Okinawa 905 0227, Japan
    Biochem Biophys Res Commun 332:1073-80. 2005
    ..Therefore, Ad4BP/SF-1 probably acts as an important indirect regulator of oocyte growth and maturation at female-phase of serial sex changing gobiid fish T. okinawae...
  83. ncbi Spontaneous mutations in the ammonium transport gene AMT4 of Chlamydomonas reinhardtii
    Kwang-Seo Kim
    Department of Plant and Microbial Biology, University of California, Berkeley, 94720, USA
    Genetics 170:631-44. 2005
    ..They indicated that the physiological substrates for Amt and Rh proteins, the only two members of their protein superfamily, are NH(3) and CO(2), respectively...
  84. ncbi Internal translation initiation mediated by the angiogenic factor Tie2
    Eun Hee Park
    Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
    J Biol Chem 280:20945-53. 2005
    ..Our data provide a framework for understanding how Tie2 mRNA is translated despite a cumbersome structured 5'-UTR and how its production is secured under unfavorable environmental conditions...
  85. ncbi Silencing of human c-myc oncogene expression by poly-DNP-RNA
    Long Shen
    Bioenergetics Laboratory, Natural Sciences Complex, University at Buffalo, Buffalo, NY 14260, USA
    Oligonucleotides 15:23-35. 2005
    ..Here, we report the synthesis of an antisense RNA inhibitor based on a new 21-nt sequence on a poly- DNP-RNA platform that can specifically inhibit cancer cell ..
  86. ncbi Selective expression of a splice variant of decay-accelerating factor in c-erbB-2-positive mammary carcinoma cells showing increased transendothelial invasiveness
    Burkhard Brandt
    Institute of Clinical Chemistry and Laboratory Medicine, University of Muenster, Germany
    Biochem Biophys Res Commun 329:318-23. 2005
    ..Using a radioactive RNA-in situ hybridisation on freshly frozen tissue microarrays and RT-PCR on native tumour tissue, the expression of ..
  87. ncbi Drosophila mitochondrial transcription factor B1 modulates mitochondrial translation but not transcription or DNA copy number in Schneider cells
    Yuichi Matsushima
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 1319, USA
    J Biol Chem 280:16815-20. 2005
    We report the cloning and molecular analysis of Drosophila mitochondrial transcription factor (d-mtTF) B1. An RNA interference (RNAi) construct was designed that reduces expression of d-mtTFB1 to 5% of its normal level in Schneider cells...
  88. ncbi A novel hematopoietic granulin induces proliferation of goldfish (Carassius auratus L.) macrophages
    Patrick C Hanington
    Department of Biological Sciences, CW-405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G E9, Canada
    J Biol Chem 281:9963-70. 2006
    ..These results indicate that goldfish granulin is a growth factor that positively modulates cell proliferation at distinct junctures of macrophage differentiation...
  89. ncbi A ternary complex of transcription factors, Nishéd and NFATc4, and co-activator p300 bound to an intronic sequence, intronic regulatory element, is pivotal for the up-regulation of myosin light chain-2v gene in cardiac hypertrophy
    Sumy Mathew
    Department of Anatomy and Cell Biology, Center for Cardiovascular and Muscle Research, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
    J Biol Chem 279:41018-27. 2004
    ....
  90. ncbi Rat connexins 30.3 and 31 are expressed in the kidney
    M A Tucker
    Department of Pathology, Harbor UCLA Medical Center, Torrance 90509
    Exp Cell Res 213:224-30. 1994
    ..3 and rCx 31, that have not previously been shown to be expressed in the rat kidney. Furthermore, rCx 30.3 utilizes two distinct transcripts in the kidney, while rCx 31 utilizes two transcripts in skin but only one in the kidney...
  91. ncbi RT-PCR analysis of 5' to 3'-end-ligated mRNAs identifies the extremities of cox2 transcripts in pea mitochondria
    Josef Kuhn
    Molekulare Botanik, , Albert-Einstein-Allee 11, 89069 Ulm, Germany
    Nucleic Acids Res 30:439-46. 2002
    Gene expression in plant mitochondria is still inadequately analyzed. To learn more about transcription and RNA processing in plant mitochondria, the 5'- and 3'-RNA extremities and the promoters of the cytochrome oxidase gene (cox2) were ..
  92. ncbi A trypanosome mitochondrial RNA polymerase is required for transcription and replication
    Jayleen Grams
    Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama, Birmingham, Alabama 35294, USA
    J Biol Chem 277:16952-9. 2002
    ..Here we report the identification and functional characterization of a mitochondrial RNA polymerase (mtRNAP) from Trypanosoma brucei, the first trans-acting factor involved in kinetoplast mitochondrial ..
  93. ncbi Unique molecular architecture of silk fibroin in the waxmoth, Galleria mellonella
    Michal Zurovec
    Institute of Entomology, Academy of Sciences, and the Faculty of Biological Sciences, University of South Bohemia, , , Czech Republic
    J Biol Chem 277:22639-47. 2002
    ..mellonella larvae within bee cultures requires continuous production of silk that must be both strong and elastic. The spectacular arrangement of the repetitive H-fibroin region apparently evolved to meet these requirements...
  94. ncbi The major subacrosomal occupant of bull spermatozoa is a novel histone H2B variant associated with the forming acrosome during spermiogenesis
    Ritu B Aul
    Department of Anatomy and Cell Biology, Queen s University, Kingston, Ontario, Canada, K7L 3N6
    Dev Biol 242:376-87. 2002
    ..Considering its developmental and molecular characteristics, we have postulated roles of SubH2Bv in acrosome assembly and acrosome-nuclear docking...
  95. ncbi DLP, a novel Dim1 family protein implicated in pre-mRNA splicing and cell cycle progression
    Xiaojing Sun
    Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 38 Xue Yuan Road, Beijing 100083, China
    J Biol Chem 279:32839-47. 2004
    ..Collectively, our experiments indicated that DLP is implicated in not only cell cycle progression but also in a more specific molecular process such as pre-mRNA splicing...
  96. ncbi Isolation and functional analysis of the mouse RXRgamma1 gene promoter in anterior pituitary cells
    Nicole B McDermott
    Department of Medicine, University of Colorado Health Sciences Center, University of Colorado Cancer Center, Denver, Colorado 80262, USA
    J Biol Chem 277:36839-44. 2002
    ..Isolation and characterization of the mouse RXRgamma1 promoter region provides a tool for further investigation focusing on thyrotrope-specific gene expression as well as negative regulation of genes by retinoic acid...
  97. ncbi Post-transcriptional control of chloroplast gene expression. Accumulation of stable psaC mRNA is due to downstream RNA cleavages in the ndhD gene
    Eva M Del Campo
    Department of Plant Biology, University of Alcal, , 28871 Madrid, Spain
    J Biol Chem 277:36457-64. 2002
    ..Hence, post-transcriptional control acts by promoting the ndhD cleavage alternative, which allows the accumulation of psaC mRNA at the expense of ndhD mRNA levels...
  98. ncbi Cloning and expression analysis of two mucin-like genes encoding microfilarial sheath surface proteins of the parasitic nematodes Brugia and Litomosoides
    Jörg Hirzmann
    Institute of Parasitology, Giessen, Germany
    J Biol Chem 277:47603-12. 2002
    ..sigmodontis genes. The core promoter regions are remarkably conserved between the paralogue genes Ls-shp3a and Ls-shp3 and their orthologues in Brugia, implicating conserved regulatory elements...
  99. ncbi The major subacrosomal occupant of bull spermatozoa is a novel histone H2B variant associated with the forming acrosome during spermiogenesis
    R B Aul
    Department of Anatomy and Cell Biology, Queen s University, Kingston, Ontario, Canada, K7L 3N6
    Dev Biol 239:376-87. 2001
    ..Considering its developmental and molecular characteristics, we have postulated roles of SubH2Bv in acrosome assembly and acrosome-nuclear docking...
  100. ncbi In Caenorhabditis elegans, the RNA-binding domains of the cytoplasmic polyadenylation element binding protein FOG-1 are needed to regulate germ cell fates
    S W Jin
    Department of Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 159:1617-30. 2001
    ..Our analyses of fog-1 mutations indicate that each of the three RNA-binding domains of FOG-1 is essential for activity...
  101. ncbi The Bax inhibitor-1 gene is differentially regulated in adult testis and developing lung by two alternative TATA-less promoters
    J C Jean
    The Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts 02118, USA
    Genomics 57:201-8. 1999
    ..Since Bax inhibitor-1 functions as a suppressor of apoptosis, its expression could provide a survival advantage for select cell populations during the peak period of apoptosis that occurs at birth...

Research Grants82

  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. Development of tools for structural genomics of viral RNA
    JEFFREY KIEFT; Fiscal Year: 2007
    Structured RNA sequences play direct roles in many viral diseases. Any effort to combat established or emerging viral threats (such as SARS, Dengue, Yellow Fever, Hanta, West Nile, HCV, etc...
  3. 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...
  4. 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 ..
  5. 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...
  6. 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...
  7. 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 ..
  8. 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 ..
  9. Structural Studies of RNA Maturation and Processing
    Christopher D Lima; Fiscal Year: 2010
    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 polyadenylation of non-coding RNA...
  10. 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...
  11. 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...
  12. 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 ..
  13. 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 ..
  14. 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 ..
  15. 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 ..
  16. 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...
  17. 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...
  18. 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...
  19. Evaluation of RNA transport elements in HIV-1 vectors
    SRINIVAS KUMAR; Fiscal Year: 2007
    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 ..
  20. Protein determinants of deltaretrovirus RNA packaging
    LOUIS MANSKY; Fiscal Year: 2007
    ..To date, the candidate's research has made a substantial contribution to the understanding of retrovirus RNA packaging...
  21. FUNCTION OF THE KINETOPLAST IN THE HEMOFLAGELLATES
    Larry Simpson; Fiscal Year: 2011
    DESCRIPTION (provided by applicant): U-insertion/deletion RNA editing is a unique post-transcriptional RNA modification process occurring in the mitochondria of trypanosomatid parasites...
  22. Coronavirus RNA Replication
    DAVID BRIAN; Fiscal Year: 2009
    Coronaviruses, with the largest known viral RNA genome, infect birds and mammals, including humans, and cause diseases ranging from subclinical to lethal...
  23. RNA Modification Enzymes: Methyltransferase/psi-synthase
    Robert M Stroud; Fiscal Year: 2010
    ..modified both during and after synthesis, thereby altering the stability, higher-order structure, and activity of RNA through changes in base stacking and hydrogen bonding...
  24. Characterizing RNA-metal binding by Raman spectroscopy
    Paul Carey; Fiscal Year: 2009
    b>RNA participates in a wide range of biological processes. In addition to its role in information transfer in the genetic code, it can act as a structural scaffold, a catalytic enzyme, or a regulatory signal...
  25. Mechanisms of RNA binding and remodeling proteins
    KEVIN D contact RANEY; Fiscal Year: 2010
    Mechanisms of RNA binding and remodeling proteins Abstract Manipulation of RNA requires the action of RNA binding proteins and ATP-dependent, molecular motor proteins that are believed to transport, remodel, and unwind secondary ..
  26. 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...
  27. Mechanisms of RNA binding and remodeling proteins
    KEVIN RANEY; Fiscal Year: 2009
    Mechanisms of RNA binding and remodeling proteins Abstract Manipulation of RNA requires the action of RNA binding proteins and ATP-dependent, molecular motor proteins that are believed to transport, remodel, and unwind secondary ..
  28. 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...
  29. Regulation of Sindbis Virus Subgenomic RNA Synthesis
    Victor Stollar; Fiscal Year: 2007
    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...
  30. Interaction between RNA interference and RNA editing pathways
    Kazuko Nishikura; Fiscal Year: 2010
    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)...
  31. Cis-acting RNA elements in hepatitis C virus replication
    Guangxiang Luo; Fiscal Year: 2003
    ..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 3' ..
  32. Cis-acting RNA elements in hepatitis C virus replication
    Guangxiang Luo; Fiscal Year: 2006
    ..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 3' ..
  33. 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 3' ..
  34. EFFECTORS AND IINHIBITORS OF SARS VIRUS POLYMERASE
    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 ..
  35. MOLECULAR BIOLOGY OF POLIOVIRUS RNA REPLICATION
    JAMES FLANEGAN; Fiscal Year: 2003
    ..Poliovirus is one of a large number of important pathogens in the Picornaviridae family of positive strand RNA viruses. The molecular mechanisms involved in poliovirus RNA replication will be examined in this study...