Differential Recruitment of the Splicing Machinery during Transcription Predicts Genome-Wide Patterns of mRNA Splicing

Molecular Cell - Tập 24 - Trang 903-915 - 2006
Michael J. Moore1, Elissa M. Schwartzfarb1, Pamela A. Silver1, Michael C. Yu1
1Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115

Tài liệu tham khảo

Abruzzi, 2004, Biochemical analysis of TREX complex recruitment to intronless and intron-containing yeast genes, EMBO J., 23, 2620, 10.1038/sj.emboj.7600261 Ares, 1999, A handful of intron-containing genes produces the lion's share of yeast mRNA, RNA, 5, 1138, 10.1017/S1355838299991379 Black, 2003, Mechanisms of alternative pre-messenger RNA splicing, Annu. Rev. Biochem., 72, 291, 10.1146/annurev.biochem.72.121801.161720 Casolari, 2004, Genome-wide localization of the nuclear transport machinery couples transcriptional status to nuclear organization, Cell, 117, 427, 10.1016/S0092-8674(04)00448-9 Casolari, 2005, Developmentally induced changes in transcriptional program alter spatial organization across chromosomes, Genes Dev., 19, 1188, 10.1101/gad.1307205 Chan, 2003, The Prp19-associated complex in spliceosome activation, Science, 302, 279, 10.1126/science.1086602 Dabeva, 1986, Autogenous regulation of splicing of the transcript of a yeast ribosomal protein gene, Proc. Natl. Acad. Sci. USA, 83, 5854, 10.1073/pnas.83.16.5854 Das, 2006, Functional coupling of RNAPII transcription to spliceosome assembly, Genes Dev., 20, 1100, 10.1101/gad.1397406 Davis, 2000, Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulates genes of yeast, Nucleic Acids Res., 20, 2176 Engebrecht, 1991, Meiosis-specific RNA splicing in yeast, Cell, 66, 1257, 10.1016/0092-8674(91)90047-3 Fan, 2001, High-copy number expression of Sub2p, a member of the RNA helicase superfamily, suppresses hpr1-mediated genomic instability, Mol. Cell. Biol., 16, 5459, 10.1128/MCB.21.16.5459-5470.2001 Fleckner, 1997, U2AF65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction, Genes Dev., 11, 1864, 10.1101/gad.11.14.1864 Galy, 2004, Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1, Cell, 116, 63, 10.1016/S0092-8674(03)01026-2 Gornemann, 2005, Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex, Mol. Cell, 19, 53, 10.1016/j.molcel.2005.05.007 Guisbert, 2005, Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profiles, RNA, 11, 383, 10.1261/rna.7234205 Guthrie, 1991 Herold, 2003, Genome-wide analysis of nuclear mRNA export pathways in Drosophila, EMBO J., 22, 2472, 10.1093/emboj/cdg233 Hieronymus, 2003, Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery, Nat. Genet., 33, 155, 10.1038/ng1080 Hieronymus, 2004, A systems view of mRNP biology, Genes Dev., 18, 2845, 10.1101/gad.1256904 Hieronymus, 2004, Genome-wide mRNA surveillance is coupled to mRNA export, Genes Dev., 18, 2652, 10.1101/gad.1241204 Holstege, 1998, Dissecting the regulatory circuitry of a eukaryotic genome, Cell, 95, 717, 10.1016/S0092-8674(00)81641-4 Houseley, 2006, RNA-quality control by the exosome, Nat. Rev. Mol. Cell Biol., 7, 529, 10.1038/nrm1964 Howe, 2003, Perturbation of transcription elongation influences fidelity of internal exon inclusion in Saccharomyces cerevisiae, RNA, 9, 993, 10.1261/rna.5390803 Jensen, 2001, The DECD box putative ATPase Sub2p is an early mRNA export factor, Curr. Biol., 11, 1711, 10.1016/S0960-9822(01)00529-2 Kadener, 2002, Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation, Proc. Natl. Acad. Sci. USA, 99, 8185, 10.1073/pnas.122246099 Kistler, 2001, Deletion of MUD2, the yeast homolog of U2AF65, can bypass the requirement for Sub2, an essential spliceosomal ATPase, Genes Dev., 15, 42, 10.1101/gad.851301 Knop, 1999, Epitope tagging of yeast genes using a PCR-based strategy: more tags and improved practical routines, Yeast, 15, 963, 10.1002/(SICI)1097-0061(199907)15:10B<963::AID-YEA399>3.0.CO;2-W Kotovic, 2003, Cotranscriptional recruitment of the U1 snRNP to intron-containing genes in yeast, Mol. Cell. Biol., 23, 5768, 10.1128/MCB.23.16.5768-5779.2003 Lacadie, 2005, Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5′ss base pairing in yeast, Mol. Cell, 19, 65, 10.1016/j.molcel.2005.05.006 Lacadie, 2006, In vivo commitment to yeast co-transcriptional splicing is sensitive to transcriptional elongation mutants, Genes Dev., 20, 2055, 10.1101/gad.1434706 Lei, 2002, Intron status and 3′-end formation control co-transcriptional export of mRNA, Genes Dev., 16, 2761, 10.1101/gad.1032902 Leu, 1999, Splicing of the meiosis-specific HOP2 transcript utilizes a unique 5′ splice site, Mol. Cell. Biol., 19, 7933, 10.1128/MCB.19.12.7933 Lewis, 1996, A yeast cap binding complex (yCBC) acts at an early step in pre-mRNA splicing, Nucleic Acids Res., 24, 3332, 10.1093/nar/24.17.3332 Libri, 2001, Multiple roles for the yeast SUB2/yUAP56 gene in splicing, Genes Dev., 15, 36, 10.1101/gad.852101 Lindstrom, 2003, Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5 associated proteins, Mol. Cell. Biol., 23, 1368, 10.1128/MCB.23.4.1368-1378.2003 Listerman, 2006, Co-transcriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells, Nat. Struct. Mol. Biol., 9, 815, 10.1038/nsmb1135 Longtine, 1998, Additional modules for versatile and economical gene deletion and modification in Saccharomyces cerevisiae, Yeast, 14, 953, 10.1002/(SICI)1097-0061(199807)14:10<953::AID-YEA293>3.0.CO;2-U Maitlin, 2005, Understanding alternative splicing: towards a cellular code, Nat. Rev. Mol. Cell Biol., 6, 386, 10.1038/nrm1645 Maniatis, 2002, An extensive network of coupling among gene expression machines, Nature, 416, 499, 10.1038/416499a Menees, 1992, MEI4, a meiosis-specific yeast gene required for chromosome synapsis, Mol. Cell. Biol., 12, 1340, 10.1128/MCB.12.3.1340 Neugebauer, 2002, On the importance of being co-transcriptional, J. Cell Sci., 115, 3865, 10.1242/jcs.00073 Preker, 2006, Autoregulation of the mRNA export factor Yra1p requires inefficient splicing of its pre-mRNA, RNA, 12, 994, 10.1261/rna.6706 Reed, 2003, Coupling transcription, splicing, and mRNA export, Curr. Opin. Cell Biol., 15, 326, 10.1016/S0955-0674(03)00048-6 Rodriguez-Navarro, 2002, An intron in the YRA1 gene is required to control Yra1 protein expression and mRNA export in yeast, EMBO Rep., 3, 438, 10.1093/embo-reports/kvf091 Rutz, 1999, Transient interaction of BBP/ScSF1 and Mud2 with the splicing machinery affects the kinetics of spliceosome assembly, RNA, 5, 819, 10.1017/S1355838299982286 Schwer, 2001, A new twist on RNA helicases: DExH/D box proteins as RNPases, Nat. Struct. Mol. Biol., 8, 113, 10.1038/84091 Spingola, 2000, A Yeast intronic splicing enhancer and Nam8p are required for Mer1p-activated splicing, Mol. Cell, 6, 329, 10.1016/S1097-2765(00)00033-2 Staley, 1998, Mechanical devices of the spliceosome: motors, clocks, springs and things, Cell, 92, 315, 10.1016/S0092-8674(00)80925-3 Stein, 1998, Functional comparison of the yeast scERV1 and scERV2 genes, Yeast, 14, 171, 10.1002/(SICI)1097-0061(19980130)14:2<171::AID-YEA209>3.0.CO;2-U Strasser, 2001, Splicing factor Sub2p is required for nuclear mRNA export through its interaction with Yra1p, Nature, 413, 648, 10.1038/35098113 Strasser, 2002, TREX is a conserved complex coupling transcription with messenger RNA export, Nature, 417, 304, 10.1038/nature746 Will, 2001, Spliceosomal UsnRNP biogenesis, structure, and function, Curr. Opin. Cell Biol., 13, 290, 10.1016/S0955-0674(00)00211-8 Xu, 2004, Prp5 bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA, EMBO J., 23, 376, 10.1038/sj.emboj.7600050 Yost, 1986, RNA splicing is interrupted by heat shock and is rescued by heat shock protein synthesis, Cell, 45, 185, 10.1016/0092-8674(86)90382-X Yu, 2004, Arginine methyltransferase affects interactions and recruitment of mRNA processing and export factors, Genes Dev., 18, 2024, 10.1101/gad.1223204 Zhang, 2001, Identification and characterization of yUAP/Sub2p, a yeast homolog of the essential human pre-mRNA splicing factor hUAP56, Genes Dev., 15, 30, 10.1101/gad.851701