rna splice sites

Summary

Summary: Nucleotide sequences located at the ends of exons and recognized in pre-messenger RNA by SPLICESOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.

Top Publications

  1. ncbi Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    Qun Pan
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
    Nat Genet 40:1413-5. 2008
  2. ncbi The spliceosome: design principles of a dynamic RNP machine
    Markus C Wahl
    Makromolekulare Röntgenkristallographie, Max Planck Institut fur biophysikalische Chemie, Am Fassberg 11, D 37077 Gottingen, Germany
    Cell 136:701-18. 2009
  3. pmc Human Splicing Finder: an online bioinformatics tool to predict splicing signals
    François Olivier Desmet
    INSERM, U827, Montpellier, France
    Nucleic Acids Res 37:e67. 2009
  4. ncbi Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    Gene Yeo
    Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue Building 68 223, Cambridge, MA 02319, USA
    J Comput Biol 11:377-94. 2004
  5. pmc MapSplice: accurate mapping of RNA-seq reads for splice junction discovery
    Kai Wang
    Department of Computer Science, University of Kentucky, Lexington, KY 40506, USA
    Nucleic Acids Res 38:e178. 2010
  6. ncbi A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
    Marc Sultan
    Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Science 321:956-60. 2008
  7. ncbi Alternative splicing and evolution: diversification, exon definition and function
    Hadas Keren
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nat Rev Genet 11:345-55. 2010
  8. pmc Noisy splicing drives mRNA isoform diversity in human cells
    Joseph K Pickrell
    Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 6:e1001236. 2010
  9. ncbi GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    Thomas D Wu
    Department of Bioinformatics Genentech, Inc, South San Francisco, CA 94080, USA
    Bioinformatics 21:1859-75. 2005
  10. ncbi Gene prediction with a hidden Markov model and a new intron submodel
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Universitat Gottingen, Gottingen, Germany
    Bioinformatics 19:ii215-25. 2003

Research Grants

  1. REGULATION OF SPLICE SITE CHOICE IN C. ELEGANS
    ALAN ZAHLER; Fiscal Year: 2009
  2. THREE SPLICE-SITE OF A SELF-SPLICING GROUP I INTRON
    Richard Waring; Fiscal Year: 1993
  3. FUNCTIONAL SPLICEOSOME AND EXTRINSIC SPLICING FACTORS
    Ren Jang Lin; Fiscal Year: 2006
  4. PROCESSING OF PRECURSORS TO MRNA IN DROSPHILA
    STEPHEN MOUNT; Fiscal Year: 1999
  5. FUNCTION OF SNRNP PARTICLES IN PRE-MRNA SPLICING
    Brian Rymond; Fiscal Year: 1993
  6. MECHANISMS OF PREMRNA SPLICING
    THOMAS MANIATIS; Fiscal Year: 2001
  7. U1 snRNP and splice site recognition in vertebrate cells
    TIMOTHY NILSEN; Fiscal Year: 2006
  8. SPLICEOSOME ASSEMBLY AND FUNCTION
    Alan Weiner; Fiscal Year: 2001
  9. FUNCTION OF SNRNP PROTEINS IN SPLICING
    PAUL SILICIANO; Fiscal Year: 2000
  10. PROCESSING OF EUKARYOTIC MESSENGER RNA
    Mary Edmonds; Fiscal Year: 1990

Detail Information

Publications349 found, 100 shown here

  1. ncbi Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    Qun Pan
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
    Nat Genet 40:1413-5. 2008
    ..From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels...
  2. ncbi The spliceosome: design principles of a dynamic RNP machine
    Markus C Wahl
    Makromolekulare Röntgenkristallographie, Max Planck Institut fur biophysikalische Chemie, Am Fassberg 11, D 37077 Gottingen, Germany
    Cell 136:701-18. 2009
    ....
  3. pmc Human Splicing Finder: an online bioinformatics tool to predict splicing signals
    François Olivier Desmet
    INSERM, U827, Montpellier, France
    Nucleic Acids Res 37:e67. 2009
    ..HSF could thus represent a valuable resource for research, diagnostic and therapeutic (e.g. therapeutic exon skipping) purposes as well as for global studies, such as the GEN2PHEN European Project or the Human Variome Project...
  4. ncbi Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    Gene Yeo
    Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue Building 68 223, Cambridge, MA 02319, USA
    J Comput Biol 11:377-94. 2004
    ..Our best models out-perform previous probabilistic models in the discrimination of human 5' (donor) and 3' (acceptor) splice sites from decoys. Finally, we discuss mechanistically motivated ways of comparing models...
  5. pmc MapSplice: accurate mapping of RNA-seq reads for splice junction discovery
    Kai Wang
    Department of Computer Science, University of Kentucky, Lexington, KY 40506, USA
    Nucleic Acids Res 38:e178. 2010
    ..These combined results indicate that MapSplice is a highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. Software download URL: http://www.netlab.uky.edu/p/bioinfo/MapSplice...
  6. ncbi A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
    Marc Sultan
    Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Science 321:956-60. 2008
    ..A global survey of messenger RNA splicing events identified 94,241 splice junctions (4096 of which were previously unidentified) and showed that exon skipping is the most prevalent form of alternative splicing...
  7. ncbi Alternative splicing and evolution: diversification, exon definition and function
    Hadas Keren
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nat Rev Genet 11:345-55. 2010
    ....
  8. pmc Noisy splicing drives mRNA isoform diversity in human cells
    Joseph K Pickrell
    Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 6:e1001236. 2010
    ..7% and show that introns in highly expressed genes are spliced more accurately, likely due to their shorter length. These results implicate noisy splicing as an important property of genome evolution...
  9. ncbi GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    Thomas D Wu
    Department of Bioinformatics Genentech, Inc, South San Francisco, CA 94080, USA
    Bioinformatics 21:1859-75. 2005
    ....
  10. ncbi Gene prediction with a hidden Markov model and a new intron submodel
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Universitat Gottingen, Gottingen, Germany
    Bioinformatics 19:ii215-25. 2003
    ..Gene finding programs have achieved relatively high accuracy on short genomic sequences but do not perform well on longer sequences with an unknown number of genes in them. Here existing programs tend to predict many false exons...
  11. ncbi hnRNP A1 proofreads 3' splice site recognition by U2AF
    João Paulo Tavanez
    Centre de Regulacio Genomica, Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
    Mol Cell 45:314-29. 2012
    ..Consistent with the functional relevance of this activity for splicing, proofreading assays reveal a role for hnRNP A1 in U2AF-mediated recruitment of U2 snRNP to the pre-mRNA...
  12. ncbi Genome-wide analyses of alternative splicing in plants: opportunities and challenges
    W Brad Barbazuk
    Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
    Genome Res 18:1381-92. 2008
    ..This review summarizes recent analyses of AS in plants, discusses the importance of further analysis, and suggests directions for future efforts...
  13. pmc Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution
    Daniel A Pomeranz Krummel
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nature 458:475-80. 2009
    ..The structure of U1 snRNP provides insights into U1 snRNP assembly and suggests a possible mechanism of 5'-splice-site recognition...
  14. pmc Detection of splice junctions from paired-end RNA-seq data by SpliceMap
    Kin Fai Au
    Department of Statistics, Stanford University, Stanford, CA 94305, USA
    Nucleic Acids Res 38:4570-8. 2010
    ..Compared to current methods, SpliceMap can achieve 12% higher sensitivity without sacrificing specificity...
  15. pmc The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin
    Walter N Moss
    Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
    PLoS ONE 7:e38323. 2012
    ..The results suggest that segment 7 mRNA splicing can be controlled by a conformational switch that exposes or hides the splice site...
  16. ncbi Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF
    Cameron D Mackereth
    Institute of Structural Biology, Helmholtz Zentrum Munchen, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    Nature 475:408-11. 2011
    ..Similar mechanisms of cooperative multi-domain conformational selection may operate more generally in the recognition of degenerate nucleotide or amino acid motifs by multi-domain proteins...
  17. ncbi Regulation of alternative splicing by reversible protein phosphorylation
    Stefan Stamm
    Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, 741 South Limestone, Lexington, KY 40536 0509, USA
    J Biol Chem 283:1223-7. 2008
    ..This knowledge can be applied to human diseases that are caused by the selection of wrong splice sites...
  18. pmc SplicePort--an interactive splice-site analysis tool
    Rezarta Islamaj Dogan
    Computer Science Department, University of Maryland, College Park, Maryland 20742, USA
    Nucleic Acids Res 35:W285-91. 2007
    ..The SplicePort web server can be accessed at http://www.cs.umd.edu/projects/SplicePort and http://www.spliceport.org...
  19. ncbi Genomic variants in exons and introns: identifying the splicing spoilers
    Franco Pagani
    International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
    Nat Rev Genet 5:389-96. 2004
  20. pmc Intronic CA-repeat and CA-rich elements: a new class of regulators of mammalian alternative splicing
    Jingyi Hui
    Institut fur Biochemie, Justus Liebig Universitat Giessen, Giessen, Germany
    EMBO J 24:1988-98. 2005
    ..HnRNP L was detected specifically bound to these diverse CA elements. These data demonstrated that intronic CA sequences constitute novel and widespread regulatory elements of alternative splicing...
  21. ncbi Nonclassical splicing mutations in the coding and noncoding regions of the ATM Gene: maximum entropy estimates of splice junction strengths
    Laura Eng
    Department of Pathology and Laboratory Medicine, The David Geffen School of Medicine at UCLA, Los Angeles, California 90095 1732, USA
    Hum Mutat 23:67-76. 2004
    ..This may lead to further misinterpretation of genotype-phenotype correlations and may subsequently impact upon gene-based therapeutic approaches...
  22. pmc TrueSight: a new algorithm for splice junction detection using RNA-seq
    Yang Li
    Department of Bioengineering, Institute for Genomic Biology, Department of Entomology, University of Illinois at Urbana Champaign, IL 61801, USA
    Nucleic Acids Res 41:e51. 2013
    ..By utilizing gene models improved by TrueSight, we characterized AS types in honey bee transcriptome. We believe that TrueSight will be highly useful to comprehensively study the biology of alternative splicing...
  23. pmc Multiple ASF/SF2 sites in the human papillomavirus type 16 (HPV-16) E4-coding region promote splicing to the most commonly used 3'-splice site on the HPV-16 genome
    Monika Somberg
    Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, Sweden
    J Virol 84:8219-30. 2010
    ..High levels of ASF/SF2 may therefore be a requirement for progression to cervical cancer. This is supported by our earlier findings that ASF/SF2 is overexpressed in high-grade cervical lesions and cervical cancer...
  24. ncbi Exon and intron definition in pre-mRNA splicing
    Laura De Conti
    International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
    Wiley Interdiscip Rev RNA 4:49-60. 2013
    ..Therefore, it is expected that future challenges in splicing research will be the careful characterization of all these influences to improve our ability to predict splicing choices in different organisms or in specific contexts...
  25. ncbi The spliceosome: a self-organized macromolecular machine in the nucleus?
    José Rino
    Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649 028 Lisboa, Portugal
    Trends Cell Biol 19:375-84. 2009
    ....
  26. pmc Insights into the selective activation of alternatively used splice acceptors by the human immunodeficiency virus type-1 bidirectional splicing enhancer
    Corinna Asang
    Institut fur Virologie, Universitatsklinikum Dusseldorf, Universitatsstr 1, D 40225 Dusseldorf, Germany
    Nucleic Acids Res 36:1450-63. 2008
    ....
  27. pmc PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data
    Yanju Zhang
    Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
    Bioinformatics 28:479-86. 2012
    ..In RNA-Seq, the exact nature of splicing events is buried in the reads that span exon-exon boundaries. The accurate and efficient mapping of these reads to the reference genome is a major challenge...
  28. pmc DNA double-strand break repair and the evolution of intron density
    Ashley Farlow
    Institute of Population Genetics, Vetmeduni Vienna, Austria
    Trends Genet 27:1-6. 2011
    ..We propose a novel framework in which species-specific differences in the activity of NHEJ and homologous recombination (HR) during the repair of DSBs underlie changes in intron density...
  29. ncbi Nucleosome positioning as a determinant of exon recognition
    Hagen Tilgner
    Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
    Nat Struct Mol Biol 16:996-1001. 2009
    ..Our analysis provides a framework that contributes to the understanding of splicing on the basis of chromatin architecture...
  30. pmc DBASS3 and DBASS5: databases of aberrant 3'- and 5'-splice sites
    Emanuele Buratti
    International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
    Nucleic Acids Res 39:D86-91. 2011
    ..DBASS3 and DBASS5 are freely available at http://www.dbass.org.uk/...
  31. pmc Conserved RNA secondary structures promote alternative splicing
    Peter J Shepard
    Department of Microbiology and Molecular Genetics, Institute for Genomics and Bioinformatics, University of California at Irvine, Irvine, California 92697 4025, USA
    RNA 14:1463-9. 2008
    ..Their frequent involvement with alternative splicing demonstrates that RNA structure formation is an important mechanism regulating gene expression and disease...
  32. pmc HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data
    Michelle T Dimon
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 5:e13875. 2010
    ..However, transcriptome sequencing creates a new class of alignment problem: mapping short reads that span exon-exon junctions back to the reference genome, especially in the case where a splice junction is previously unknown...
  33. pmc Dynamic regulation of alternative splicing by silencers that modulate 5' splice site competition
    Yang Yu
    Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
    Cell 135:1224-36. 2008
    ..The data indicate that perturbations of non-rate-limiting step(s) in splicing can lead to dramatic shifts in splice site choice...
  34. pmc Biased chromatin signatures around polyadenylation sites and exons
    Noah Spies
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Mol Cell 36:245-54. 2009
    ..Together, these findings provide evidence for extensive functional connections between chromatin structure and RNA processing...
  35. pmc U12DB: a database of orthologous U12-type spliceosomal introns
    Tyler S Alioto
    Genome Bioinformatics Laboratory, Center for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Spain
    Nucleic Acids Res 35:D110-5. 2007
    ..Public access to the U12DB is available at http://genome.imim.es/cgi-bin/u12db/u12db.cgi...
  36. pmc Defective splicing, disease and therapy: searching for master checkpoints in exon definition
    Emanuele Buratti
    International Centre for Genetic Engineering and Biotechnology ICGEB, Padriciano 99, 34012 Trieste, Italy
    Nucleic Acids Res 34:3494-510. 2006
    ..In the final part, we shall then discuss possible therapeutic targets and strategies to rescue genetic defects of complex splicing systems...
  37. ncbi Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity
    Michael Hiller
    Institute of Computer Science, Friedrich Schiller University Jena, Chair for Bioinformatics, Ernst Abbe Platz 2, 07743 Jena, Germany
    Nat Genet 36:1255-7. 2004
    ..Because of their subtle effects on mRNA and protein structures, these splice acceptors are often overlooked or underestimated, but they may have a great impact on biology and disease...
  38. pmc ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets
    Sylvain Foissac
    Centre de Regulacio Genomica, Barcelona, Spain
    Nucleic Acids Res 35:W297-9. 2007
    ..imim.es/astalavista...
  39. ncbi Exonization of transposed elements: A challenge and opportunity for evolution
    Jürgen Schmitz
    Institute of Experimental Pathology ZMBE, University of Munster, Munster, Germany
    Biochimie 93:1928-34. 2011
    ....
  40. pmc A novel splicing regulator shares a nuclear import pathway with SR proteins
    Ming Chih Lai
    Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
    EMBO J 22:1359-69. 2003
    ..Thus, a novel splicing regulator with opposite activities to SR proteins shares an identical import pathway with SR proteins to the nucleus...
  41. pmc Comparison of splice sites in mammals and chicken
    Josep F Abril
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, and Programa de Bioinformàtica i Genòmica, Centre de Regulacio Genomica, C Dr Aiguader 80, E 08003 Barcelona, Catalonia, Spain
    Genome Res 15:111-9. 2005
    ..Switching between GT-AG and the noncanonical GC-AG U2 subtypes, on the contrary, does not appear to be unusual; in particular, T to C mutations appear to be relatively well tolerated in GT-AG introns with very strong donor sites...
  42. ncbi The receptor for branch-site docking within a group II intron active site
    Stephanie Hamill
    Integrated Program in Cellular, Molecular and Biophysical Studies, Columbia University, 500 West 168th Street, New York, New York 10032, USA
    Mol Cell 23:831-40. 2006
    ..Furthermore, we show that crosslinked branch sites can carry out both steps of splicing, suggesting that the conformational state of the intron core is set early and that it persists throughout the entire splicing process...
  43. ncbi Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else?
    Jean Vincent Chamary
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Trends Genet 21:256-9. 2005
    ..Evidence for selection between synonymous codons that are associated with splicing enhancers remains after controlling for this bias, whereas support for cryptic splice-site avoidance is diminished...
  44. pmc An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells
    Gene W Yeo
    Crick Jacobs Center for Theoretical and Computational Biology, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Struct Mol Biol 16:130-7. 2009
    ..These findings suggest that FOX2 functions as a critical regulator of a splicing network, and we further show that FOX2 is important for the survival of human embryonic stem cells...
  45. pmc The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5' splice site cleavage during pre-mRNA splicing
    Prakash Koodathingal
    Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
    Mol Cell 39:385-95. 2010
    ..These data indicate that spliceosomes distinguish slow substrates and that the mechanisms for establishing the fidelity of 5' splice site cleavage and exon ligation share a common ATP-dependent framework...
  46. ncbi Characterization of BRCA1 and BRCA2 splicing variants: a collaborative report by ENIGMA consortium members
    Mads Thomassen
    Department of Clinical Genetics, Odense University Hospital, Soenderboulevard 29, 5000 Odense C, Denmark
    Breast Cancer Res Treat 132:1009-23. 2012
    ..Importantly, this study demonstrates the added value of collaboration between laboratories, and across disciplines, to collate and interpret information from clinical testing laboratories to consolidate patient management...
  47. pmc Identifying the mechanisms of intron gain: progress and trends
    Paul Yenerall
    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
    Biol Direct 7:29. 2012
    ..Finally, because these proposed mechanisms fail to explain the mechanistic origin of many recently gained introns, we also look at trends that may aid researchers in identifying other potential mechanism(s) of intron gain...
  48. ncbi Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  49. pmc Sequence features involved in the mechanism of 3' splice junction wobbling
    Kuo Wang Tsai
    Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
    BMC Mol Biol 11:34. 2010
    ..Recently, a new splice-junction wobbling mechanism was proposed that subtle modifications exist in mRNA maturation by alternatively choosing at 5'- GTNGT and 3'- NAGNAG, which created single amino acid insertion and deletion isoforms...
  50. pmc Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution
    Robert K Bradley
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    PLoS Biol 10:e1001229. 2012
    ....
  51. pmc Allele-specific recognition of the 3' splice site of INS intron 1
    Jana Kralovicova
    Division of Human Genetics, University of Southampton School of Medicine, MP808, Southampton, SO16 6YD, UK
    Hum Genet 128:383-400. 2010
    ....
  52. ncbi hnRNP H1 and intronic G runs in the splicing control of the human rpL3 gene
    Annapina Russo
    Dipartimento di Biochimica e Biotecnologie Mediche, Universita Federico II, Napoli 80131, Italy
    Biochim Biophys Acta 1799:419-28. 2010
    ..We propose a working model in which rpL3 recruits hnRNP H1 and, through cooperation with other splicing factors, promotes selection of the alternative splice site...
  53. ncbi Splicing in disease: disruption of the splicing code and the decoding machinery
    Guey Shin Wang
    Department of Pathology, Baylor College of Medicine, Houston, Texas 77030, USA
    Nat Rev Genet 8:749-61. 2007
    ..An unexpectedly large fraction of exonic mutations exhibit a primary pathogenic effect on splicing. Furthermore, normal genetic variation significantly contributes to disease severity and susceptibility by affecting splicing efficiency...
  54. ncbi Alternative splicing: multiple control mechanisms and involvement in human disease
    Javier F Caceres
    MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK
    Trends Genet 18:186-93. 2002
    ..We also focus on the role of the transcriptional machinery in the regulation of alternative splicing, and on those alterations of alternative splicing that lead to human disease...
  55. ncbi Decoding muscle alternative splicing
    Miriam Llorian
    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
    Curr Opin Genet Dev 21:380-7. 2011
    ....
  56. ncbi A novel gene from the human endogenous retrovirus K expressed in transformed cells
    Vivienne Armbruester
    Institut für Mikrobiologie und Hygiene, Abteilung Virologie, Geb 47, Universitatskliniken des Saarlandes, Homburg Saar D 66421, Germany
    Clin Cancer Res 8:1800-7. 2002
    ..We investigated the expression of human endogenous retrovirus K (HERV-K) transcripts in various tumor tissues and transformed cell lines...
  57. ncbi Estimating the neutral rate of nucleotide substitution using introns
    Michael M Hoffman
    European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, England
    Mol Biol Evol 24:522-31. 2007
    ..Although the intron method may be more useful for shorter evolutionary distances, it is less useful at longer distances due to the poor alignment of less-conserved positions...
  58. pmc Contribution of bioinformatics predictions and functional splicing assays to the interpretation of unclassified variants of the BRCA genes
    Jean Christophe Théry
    INSERM U614, IFRMP, Faculty of Medicine and Department of Genetics, University Hospital, Institute for Biomedical Research and Innovation, Rouen, France
    Eur J Hum Genet 19:1052-8. 2011
    ..This work highlights the contribution of splicing minigene assays to the assessment of pathogenicity, not only when patient RNA is not available, but also as a tool to improve the accuracy of bioinformatics predictions...
  59. ncbi Isolation of an active step I spliceosome and composition of its RNP core
    Sergey Bessonov
    Department of Cellular Biochemistry, Max Planck Institute of Biophysical Chemistry, D 37077 Gottingen, Germany
    Nature 452:846-50. 2008
    ..Our data provide insights into the spliceosome's catalytic RNP domain and indicate a central role for the aforementioned proteins in sustaining its catalytically active structure...
  60. ncbi Evaluation of in silico splice tools for decision-making in molecular diagnosis
    Claude Houdayer
    Institut Curie, Service de génétique oncologique, Paris, France
    Hum Mutat 29:975-82. 2008
    ....
  61. ncbi Intronic alterations in BRCA1 and BRCA2: effect on mRNA splicing fidelity and expression
    Xiaowei Chen
    Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Hum Mutat 27:427-35. 2006
    ..Our studies help to clarify the aberrant splicing in BRCA1 and BRCA2 as well as provide information that can be used clinically to help counsel breast/ovarian cancer prone families...
  62. ncbi Substances that can change alternative splice-site selection
    Chiranthani Sumanasekera
    Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, B283, Biomedical Biological Sciences Research Building, 741 South Limestone, Lexington, KY 40536, USA
    Biochem Soc Trans 36:483-90. 2008
    ....
  63. ncbi Transposable elements in disease-associated cryptic exons
    Igor Vorechovsky
    Division of Human Genetics, University of Southampton School of Medicine, MP808, Tremona Road, Southampton SO16 6YD, UK
    Hum Genet 127:135-54. 2010
    ....
  64. pmc Spliceosome discards intermediates via the DEAH box ATPase Prp43p
    Rabiah M Mayas
    Graduate Program in Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 107:10020-5. 2010
    ..Because Prp43p also promotes spliceosome disassembly after exon ligation, this work establishes a parallel between the discard of suboptimal intermediates and the dissociation of a genuine excised intron product...
  65. pmc Competing upstream 5' splice sites enhance the rate of proximal splicing
    Martin J Hicks
    Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697 4025, USA
    Mol Cell Biol 30:1878-86. 2010
    ..These results reveal the discovery of a new splicing regulatory element, an upstream 5' splice site functioning as a splicing enhancer...
  66. pmc Exon-trapping mediated by the human retrotransposon SVA
    Dustin C Hancks
    Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 19:1983-91. 2009
    ....
  67. pmc Dual-specificity splice sites function alternatively as 5' and 3' splice sites
    Chaolin Zhang
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Proc Natl Acad Sci U S A 104:15028-33. 2007
    ..We discuss the implications of this unusual splicing pattern for the diverse mechanisms of exon recognition and for gene evolution...
  68. ncbi ssSNPTarget: genome-wide splice-site Single Nucleotide Polymorphism database
    Jin Ok Yang
    Korean BioInformation Center KOBIC, Korea Research Institute of Bioscience and Biotechnology KRIBB, Daejeon, Korea
    Hum Mutat 30:E1010-20. 2009
    ..Users can query ssSNPTarget with several types of search terms (gene symbol, SNP rs number, transcript ID, or genomic position), and the information can be accessed at http://variome.kobic.re.kr/ssSNPTarget/ or http://ssSNPTarget.org...
  69. pmc Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes
    Schraga H Schwartz
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 18:88-103. 2008
    ....
  70. pmc Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping
    Petr Divina
    Division of Human Genetics, University of Southampton School of Medicine, Southampton, UK
    Eur J Hum Genet 17:759-65. 2009
    ..These results will facilitate phenotypic prediction of splicing mutations and provide further insights into splicing enhancer and silencer elements and their relative importance for splice-site selection in vivo...
  71. pmc Splice-site pairing is an intrinsically high fidelity process
    Kristi L Fox-Walsh
    Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697 4025, USA
    Proc Natl Acad Sci U S A 106:1766-71. 2009
    ..We conclude that all multi-intron-containing genes are alternatively spliced and that the reduction of SMN results in a general splicing defect that is mediated through alterations in the fidelity of splice-site pairing...
  72. pmc Influence of RNA secondary structure on the pre-mRNA splicing process
    Emanuele Buratti
    International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012 Trieste, Italy
    Mol Cell Biol 24:10505-14. 2004
  73. ncbi High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes
    David G Knowles
    Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland
    Mol Biol Evol 23:1548-57. 2006
    ....
  74. pmc Cooperative-binding and splicing-repressive properties of hnRNP A1
    Hazeem L Okunola
    Cold Spring Harbor Laboratory, P O Box 100, Cold Spring Harbor, NY 11724, USA
    Mol Cell Biol 29:5620-31. 2009
    ..Finally, when two distant high-affinity sites are present on the same RNA, they facilitate cooperative spreading of hnRNP A1 between the two sites...
  75. ncbi Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicing
    Michael Krawczak
    Institut für Medizinische Informatik und Statistik, Christian Albrechts Universitat, Kiel, Germany
    Hum Mutat 28:150-8. 2007
    ..6% of disease-causing missense substitutions in human genes are likely to affect the mRNA splicing phenotype. Taken together, our results are consistent with correct donor splice-site recognition being a key step in exon recognition...
  76. pmc High-throughput quantification of splicing isoforms
    Jean Philippe Brosseau
    Universite de Sherbrooke, Departement de Microbiologie et d Infectiologie Sherbrooke, Quebec J1H 5N4, Canada
    RNA 16:442-9. 2010
    ..Using this pipeline it is now possible to rapidly identify splicing isoform signatures in different types of human tissues or to validate complete sets of data generated by microarray expression profiling and deep sequencing techniques...
  77. pmc Ubiquitous internal gene duplication and intron creation in eukaryotes
    Xiang Gao
    Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 106:20818-23. 2009
    ..These results strongly suggest a major evolutionary role for internal gene duplications in the origin of genomic novelties, particularly as a mechanism for intron gain...
  78. pmc SROOGLE: webserver for integrative, user-friendly visualization of splicing signals
    Schraga Schwartz
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 37:W189-92. 2009
    ..SROOGLE is available at http://sroogle.tau.ac.il, and may also be downloaded as a desktop version...
  79. pmc A naturally occurring splicing site mutation in the Brassica rapa FLC1 gene is associated with variation in flowering time
    Yu Xiang Yuan
    Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    J Exp Bot 60:1299-308. 2009
    ..rapa accessions and in a segregating Chinese cabbage doubled-haploid population. These findings suggest that a naturally occurring splicing mutation in the BrFLC1 gene contributes greatly to flowering-time variation in B. rapa...
  80. ncbi Intron loss and gain in Drosophila
    Jasmin Coulombe-Huntington
    Department of Human Genetics, McGill University, Montreal, Quebec, Canada
    Mol Biol Evol 24:2842-50. 2007
    ....
  81. ncbi Molecular diagnosis of neurofibromatosis type 1: 2 years experience
    Sian Griffiths
    Institute of Medical Genetics, University Hospital of Wales, Cardiff CF14 4XN, UK
    Fam Cancer 6:21-34. 2007
    ....
  82. ncbi Mutation spectrum of the dystrophin gene in 442 Duchenne/Becker muscular dystrophy cases from one Japanese referral center
    Yasuhiro Takeshima
    Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
    J Hum Genet 55:379-88. 2010
    ..At one Japanese referral center, the hospital-based mutation database of the dystrophin gene was for the first time established with the highest levels of quality and patient's number...
  83. ncbi A polymorphic GT repeat from the human cardiac Na+Ca2+ exchanger intron 2 activates splicing
    N Gabellini
    Department of Biological Chemistry, University of Padova, Italy
    Eur J Biochem 268:1076-83. 2001
    ....
  84. pmc Mitogen-activated protein kinase phosphorylation of splicing factor 45 (SPF45) regulates SPF45 alternative splicing site utilization, proliferation, and cell adhesion
    Adnan M Al-Ayoubi
    Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina, USA
    Mol Cell Biol 32:2880-93. 2012
    ..These data identify SPF45 as the first splicing factor regulated by multiple MAP kinase pathways and show effects of both SPF45 overexpression and phosphorylation...
  85. pmc CEF1/CDC5 alleles modulate transitions between catalytic conformations of the spliceosome
    Charles C Query
    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    RNA 18:1001-13. 2012
    ....
  86. ncbi ERISdb: a database of plant splice sites and splicing signals
    Michał Wojciech Szcześniak
    Laboratory of Bioinformatics, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
    Plant Cell Physiol 54:e10. 2013
    ..All the data are stored in a novel database called ERISdb and are freely available at http://lemur.amu.edu.pl/share/ERISdb/...
  87. pmc RNA induces conformational changes in the SF1/U2AF65 splicing factor complex
    Ankit Gupta
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    J Mol Biol 405:1128-38. 2011
    ..We propose that the conformational changes that are induced by assembly of the SF1/U2AF(65)/RNA complex serve to position the pre-mRNA splice site optimally for subsequent stages of splicing...
  88. pmc OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds
    Jie Wu
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 41:5149-63. 2013
    ..OLego is freely available at http://zhanglab.c2b2.columbia.edu/index.php/OLego...
  89. pmc A segmental genomic duplication generates a functional intron
    Uffe Hellsten
    DOE Joint Genome Institute, Walnut Creek, California 94598, USA
    Nat Commun 2:454. 2011
    ..This experiment recapitulates in vivo the birth of an intron that arose in the ancestral jawed vertebrate lineage nearly half-a-billion years ago...
  90. pmc TassDB2 - A comprehensive database of subtle alternative splicing events
    Rileen Sinha
    Albert Ludwigs University Freiburg, Germany
    BMC Bioinformatics 11:216. 2010
    ..Towards this goal we recently set up TassDB (Tandem Splice Site DataBase, version 1), which stores data about alternative splicing events at tandem splice sites separated by 3 nt in eight species...
  91. pmc Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins
    Eric T Wang
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Cell 150:710-24. 2012
    ..These findings hold several new implications for DM pathogenesis...
  92. pmc Genetic variation in the alternative splicing regulator RBM20 is associated with dilated cardiomyopathy
    Marwan M Refaat
    Cardiovascular Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania 15213, USA
    Heart Rhythm 9:390-6. 2012
    ..Dilated cardiomyopathy (DCM) is a leading cause of heart failure and death. The etiology of DCM is genetically heterogeneous...
  93. pmc Identification of new splice sites used for generation of rev transcripts in human immunodeficiency virus type 1 subtype C primary isolates
    Elena Delgado
    Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
    PLoS ONE 7:e30574. 2012
    ..Usage of the newly identified splice sites is consistent with sequence features commonly found in subtype C viruses. These results show that splice site usage may differ between HIV-1 subtypes...
  94. ncbi Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1
    Vincent Galy
    Unité de Biologie Cellulaire du Noyau, CNRS URA 2582, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
    Cell 116:63-73. 2004
    ..We propose that at this confined site the perinuclear Mlp1 implements a quality control step prior to export, physically retaining faulty pre-mRNAs...
  95. pmc Widespread impact of nonsense-mediated mRNA decay on the yeast intronome
    Shakir Sayani
    Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095 1569, USA
    Mol Cell 31:360-70. 2008
    ..These results show that NMD has a wider impact than previously thought on the degradation of yeast-unspliced transcripts and plays an important role in discarding precursors of regulated or suboptimally spliced transcripts...
  96. pmc Variation in alternative splicing across human tissues
    Gene Yeo
    Department of Biology, Center for Biological and Computational Learning, Massachusetts Institute of Technology, Cambridge, MA 02319, USA
    Genome Biol 5:R74. 2004
    ..To compare AS events across human tissues, we analyzed the splicing patterns of genomically aligned expressed sequence tags (ESTs) derived from libraries of cDNAs from different tissues...
  97. pmc Spliceostatin A inhibits spliceosome assembly subsequent to prespliceosome formation
    Gabriel A Roybal
    Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
    Nucleic Acids Res 38:6664-72. 2010
    ..This work establishes SSA as a powerful tool for dissecting the dynamics of spliceosomes in cells. In addition our data will inform the design of synthetic splicing modulator compounds for targeted anti-tumor treatment...
  98. ncbi Genotype-phenotype analysis in 2,405 patients with a dystrophinopathy using the UMD-DMD database: a model of nationwide knowledgebase
    Sylvie Tuffery-Giraud
    Universite Montpellier 1, Faculte de Medecine, Montpellier, France
    Hum Mutat 30:934-45. 2009
    ..Finally, such a national database will prove to be useful to implement the international global DMD patients' registries under development...
  99. pmc Role of the 3' splice site in U12-dependent intron splicing
    R C Dietrich
    Department of Molecular Biology, The Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
    Mol Cell Biol 21:1942-52. 2001
    ..Furthermore, the U12-type spliceosome appears to be unable to scan for a distal 3' splice site...
  100. pmc SRp30c is a repressor of 3' splice site utilization
    Martin J Simard
    Departement de Microbiologie et d Infectiologie, Faculte de Medecine, Universite de Sherbrooke, Sherbrooke, Quebec, Canada J1H 5N4
    Mol Cell Biol 22:4001-10. 2002
    ..Our results indicate that SRp30c can function as a repressor of 3' splice site utilization and suggest that the SRp30c-CE9 interaction may contribute to the control of hnRNP A1 alternative splicing...
  101. pmc Modulation of alternative splicing by long-range RNA structures in Drosophila
    Veronica A Raker
    Center for Genomic Regulation CRG, Dr Aiguader, 88, 08003 Barcelona, Spain
    Nucleic Acids Res 37:4533-44. 2009
    ..Thus, base-pairing interactions within introns, even those occurring over long distances, are more frequent modulators of alternative splicing than is currently assumed...

Research Grants62

  1. REGULATION OF SPLICE SITE CHOICE IN C. ELEGANS
    ALAN ZAHLER; Fiscal Year: 2009
    ..3- To characterize suppressors of 5'and 3'splice site defects in order to illuminate the mechanisms of splice site selection. ..
  2. THREE SPLICE-SITE OF A SELF-SPLICING GROUP I INTRON
    Richard Waring; Fiscal Year: 1993
    ..coli in such a way that the gene is only expressed if the intron splices itself out. The competitive splice-site analysis will also be aided by this in vivo splicing assay...
  3. FUNCTIONAL SPLICEOSOME AND EXTRINSIC SPLICING FACTORS
    Ren Jang Lin; Fiscal Year: 2006
    ..We will analyze the splicing machinery when DBP2 function is impaired in vivo or in vitro. The proposed study shall reveal the dynamic features and the remodeling of the spliceosome core in yeast and human. ..
  4. PROCESSING OF PRECURSORS TO MRNA IN DROSPHILA
    STEPHEN MOUNT; Fiscal Year: 1999
    ..Additionally, at least one potential spontaineous mutation which enhances the dominant B52 phenotype has been found, although it remains unmapped. ..
  5. FUNCTION OF SNRNP PARTICLES IN PRE-MRNA SPLICING
    Brian Rymond; Fiscal Year: 1993
    ..Genetic and biochemical experiments will be performed to characterize the RNA binding properties of the 70 kd protein and to determine the contribution of the U1 snRNA/70 kd protein complex to spliceosome formation and splicing...
  6. MECHANISMS OF PREMRNA SPLICING
    THOMAS MANIATIS; Fiscal Year: 2001
    ..When completed, the proposed studies will significantly advance the understanding of the mechanisms of RNA splicing and editing. ..
  7. U1 snRNP and splice site recognition in vertebrate cells
    TIMOTHY NILSEN; Fiscal Year: 2006
    ..Furthermore, the results may be relevant to our understanding of regulated alternative splicing. ..
  8. SPLICEOSOME ASSEMBLY AND FUNCTION
    Alan Weiner; Fiscal Year: 2001
    ....
  9. FUNCTION OF SNRNP PROTEINS IN SPLICING
    PAUL SILICIANO; Fiscal Year: 2000
    ....
  10. PROCESSING OF EUKARYOTIC MESSENGER RNA
    Mary Edmonds; Fiscal Year: 1990
    ..If specific proteins are identified, their binding to the oligo U(+) mRNA population would be tested and ultimately binding to an oligo U containing mRNA such as beta-actin would be tested...
  11. REGULATION OF TISSUE-SPECIFIC RNA SPLICING IN DROSOPHILA
    A Lopez; Fiscal Year: 2002
    ..Hence, these investigations will be highly relevant to the regulation of splicing in humans. ..
  12. REGULATION OF AVIAN SARCOMA VIRUS--RNA PROCESSING
    CONRAD STOLTZFUS; Fiscal Year: 1999
    ..Because retroviruses bypass the normal requirements for complete splicing prior to transport, it will also add to the understanding of how cellular RNA,processing and transport are regulated. ..
  13. Probing the 3' Loop of U6 snRNA in Spliceosome Catalysis
    KENNETH DERY; Fiscal Year: 2005
    ..These interactions, once defined, would help our understanding of how the different sites of chemistry become tightly linked during spliceosome catalysis. ..
  14. RNA TARGETING WITH TERTIARY INTERACTIONS
    Douglas Turner; Fiscal Year: 2000
    ..Because maturation of rRNA precursor is essential for proliferation of P. carinii, and no group I self-splicing introns are known in human genes, the results could also provide potential therapeutics for P. carinii pneumonia. ..
  15. GENOMIC ANALYSIS OF ALZHEIMERS DISEASE GENES
    Gerard Schellenberg; Fiscal Year: 2002
    ..A fifth goal is to refine the location of additional AD loci using Monte Carlo simulation methods for analysis of family data. ..
  16. ASSAY SYSTEM FOR EVALUATING CELLULAR ANTISENSE DELIVERY
    Moo Cho; Fiscal Year: 1999
    ..Due to its intrinsic nature, however, ther system cannot be used with an oligomer that activates RNase H. However, this is not a limitation. ..
  17. Processing of Pre-Messenger RNA
    Susan Berget; Fiscal Year: 2005
    ..abstract_text> ..
  18. Mechanisms of 3' Splice Site Selection in S. cerevisiae
    DAVID MCPHEETERS; Fiscal Year: 2005
    ..Because these enzymes have important roles in all aspects of cellular RNA metabolism, the results of these studies will be relevant to the study of their functions in other biological contexts. ..
  19. Tangle Formation in P301L Transgenic Mice
    Michael Hutton; Fiscal Year: 2005
    ....
  20. Tool to Integrate Genomic and Proteomic Data of Aging
    ZOE LACROIX; Fiscal Year: 2002
    ..Aim 2: Enhance the access to information related to age-related diseases, disorders and disabilities through the exploration of multiple data sources. ..
  21. Functional Dissection of an F-box Protein in Development
    Michael Weir; Fiscal Year: 2006
    ..abstract_text> ..
  22. Amyloid and tau pathology in a transgenic model
    Michael Hutton; Fiscal Year: 2006
    ..abstract_text> ..
  23. A COLLABORATIVE GENOMIC STUDY OF BIPOLAR DISORDER
    Wade Berrettini; Fiscal Year: 2007
    ..Analysis of the existing sib pair families plus this large set of cases and controls should permit the confirmation of several vulnerability genes during this grant period. ..
  24. Regulation of mRNA Splicing by Mer1p
    Marc Spingola; Fiscal Year: 2007
    ..This project will elucidate how Mer1p and similar proteins function and will offer important insights towards the basis of diseases like Fragile X Syndrome in humans. [unreadable] [unreadable] [unreadable]..
  25. Analysis of Tumor RNA Variants using PMSG
    CHAOFU SHI; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  26. Consequences of lifetime isolated Growth Hormone deficiency
    Roberto Salvatori; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  27. Creation of a mouse model of isolated GH deficiency
    Roberto Salvatori; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  28. Connections between mRNA elongation and splicing
    MARIANO GARCIA BLANCO; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  29. GnRH signaling in LbetaT2 gonadotrope cells
    Nicholas Webster; Fiscal Year: 2009
    ..These genetic models will include cell-specific transgenic overexpression of selected co-repressors as well as gonadotrope-specific deletion of components of the Gs and Gq/11 pathways using cre-loxP technology. ..
  30. ADP-Ribose Polymer Metabolism in Spermatogenesis
    Ralph Meyer; Fiscal Year: 2009
    ..This research is significant because it is expected to contribute to the development of new therapeutic approaches that target ADPR polymer metabolism for the treatment of male fertility problems. ..
  31. Genomic Measurement of Alternative Splicing by DNA Array
    Douglas Black; Fiscal Year: 2008
    ..abstract_text> ..
  32. DNA Damage and Neurodegeneration in Cockayne Syndrome
    James Cleaver; Fiscal Year: 2009
    ..Successful conclusion of these studies will expand our knowledge of mechanisms of neurodegeneration and lay groundwork for development of therapeutic approaches for CS patients. ..
  33. Mechanisms of Developmentally Regulated Splicing
    Thomas Cooper; Fiscal Year: 2009
    ....
  34. RED CELL CYTOSKELETAL PROTEIN AND MITOSIS
    Shu Ching Huang; Fiscal Year: 2008
    ..Finally, we shall define the relationship between changes in the expression of these 4.1R isoforms and the transition from proliferation to post-mitotic states during erythroid differentiation. ..
  35. The Impact of Fluoride on the Rho Signaling Pathway and the Actin Cytoskeleton
    CAROLYN GIBSON; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  36. Regulation of Alternative Splicing of FGFR2 pre-mRNA
    MARIANO GARCIA BLANCO; Fiscal Year: 2008
    ..We will identify the trans-acting factors required for this inclusion using conventional biochemical methods and a new screen using siRNA libraries and fluorescence-based reporters of alternative splicing. ..
  37. 2008 Biology of Acute Respiratory Infections Gordon Research Conference
    JOSEPH MIZGERD; Fiscal Year: 2007
    ..End of Abstract) [unreadable] [unreadable] [unreadable]..
  38. Integrated instrument system for maintenance and delivery of RNAi libraries
    MARIANO GARCIA BLANCO; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  39. Variation of D. melanogaster chromosome 4
    Manyuan Long; Fiscal Year: 2006
    ..These studies should add significantly to the understanding of the evolutionary genetics of the Drosophila fourth chromosome. ..
  40. Genetics, Lipids, and Responses to Exercise Training
    Amy Halverstadt; Fiscal Year: 2006
    ..abstract_text> ..
  41. BIOCHEMISTRY OF PREMRNA SPLICING FACTORS
    David Horowitz; Fiscal Year: 2004
    ..Following these interactions through the second step of the reaction will further the understanding of the mechanism of splicing. ..
  42. MOLECULAR MECHANISMS OF CYTOCHROME P450 EXPRESSION
    CURTIS OMIECINSKI; Fiscal Year: 2002
    ....
  43. U2AF AND SPLICE SITE RECOGNITION IN C ELEGANS
    Thomas Blumenthal; Fiscal Year: 2003
    ..In order to identify additional components of the machinery needed to prevent export of RNA containing these sequences, mutants that suppress the nuclear retention phenotype will be selected in C. elegans. ..
  44. Toxicogenomics of Lead, Mercury, and Cadmium
    Douglas Ruden; Fiscal Year: 2003
    ....
  45. THE LINK BETWEEN SPLICING & EXPORT OF MESSENGER RNA
    Robin Reed; Fiscal Year: 2003
    ..Together, these studies should provide important new insights into the mechanism of mRNA export and the link between splicing and export. ..
  46. LONG QT SYNDROME--GENETIC STUDIES
    Arthur Moss; Fiscal Year: 2002
    ....
  47. COMPUTATIONAL ANALYSIS OF GENOME EXPRESSION DATA
    Michael Zhang; Fiscal Year: 2002
    ..abstract_text> ..
  48. P53-MEDIATED CHEMOSENSITIVITY IN NEUROBLASTOMA
    Linda Harris; Fiscal Year: 2002
    ..The studies proposed will assist in understanding mechanisms by which NB develop pleiotropic resistance to agents having different mechanisms of action and allow insight into new approaches to treat advanced NB. ..
  49. THERAPUTIC TRIAL IN PATIENTS WITH LQTS 3 GENE MUTATION
    Arthur Moss; Fiscal Year: 2002
    ..The significance of this work relates to the future use of molecular therapeutics to treat ion-channel disorders associated with congenital and acquired cardiac repolarization disorders. ..
  50. Dominant Mutation that Affect EGF-R Signal Transduction
    Douglas Ruden; Fiscal Year: 2003
    ..It is important to understand regulators of RTK signaling because Ras-Raf dependent neoplasia accounts for as many as one-fifth of all human cancers. ..
  51. GLUTAMATE BIOSYNTHESIS MUTANTS AND ALCOHOL SENSITIVITY
    Douglas Ruden; Fiscal Year: 2003
    ..This genetic approach would eventually lead to a better understanding to a better understanding of the genetic influences that underlie risk for alcoholism. ..
  52. Epigenetics of Dietary and Body Fat in Drosophila
    Douglas Ruden; Fiscal Year: 2006
    ..abstract_text> ..
  53. Imaging Alternative Splicing During Tumor Progression
    MARIANO GARCIA BLANCO; Fiscal Year: 2006
    ..We will employ the aforementioned imaging reporters to study the regulation of alternative splicing in living animals. We hope to provide an anatomic map of gene expression based on alternative splicing regulation. ..
  54. Consequences of generalized lack of GHRH
    Roberto Salvatori; Fiscal Year: 2005
    ..By recombinase technique, we will generate KO lines with no Neor, avoiding any interference with distant or neighboring genes. In addition, results obtained in the GHRHKO1 line will be confirmed or disproved. ..
  55. In Vitro Peptide Mass-Signature Genotyping of Tumor DNA
    CHERYL TELMER; Fiscal Year: 2004
    ..The TP53 gene will be the focus of the SBIR project, but the genotyping system that will be developed will be applicable to any gene or set of genes, whether involved in cancer or not. ..
  56. Combinatorial Approaches to Activators of the NGF Recep*
    Nicholas Webster; Fiscal Year: 2005
    ..The Specific Aim of this proposal is to screen the combinatorial asterriquinone library against the NGF receptor. ..
  57. QUANTITATIVE GENETICS OF OPIATE ADDICTION
    Wade Berrettini; Fiscal Year: 2004
    ..This may enhance our knowledge of genetic susceptibility to opioid dependence in human populations. ..
  58. A Neuropeptide Gene in Psychiatric Illness
    Wade Berrettini; Fiscal Year: 2004
    ..We have assembled sets (n>600) of parent-child trios for both SZ and BPD to test the hypothesis that variation in this gene increases risks for these disorders. These studies may identify a susceptibility gene for SZ and/or BPD. ..
  59. Cancer Genotyping by Peptide Mass Spectrometry
    CHERYL TELMER; Fiscal Year: 2004
    ..These include infectious disease, inherited disease, and pharmacogenetics. ..
  60. Molecular analysis of GHRH receptor missense mutations
    Roberto Salvatori; Fiscal Year: 2004
    ..Altogether, these experiments will teach us new information about the pathophysiology of GHRHR signaling in health and disease. ..
  61. Conference on Molecular Biology of the Heart
    Leslie Leinwand; Fiscal Year: 2002
    ..It will be a multidisciplinary meeting that should bring together people who are beginning to have regular dialogues but whose traditions have been somewhat separate. ..