A Genome-Wide Analysis Indicates that Yeast Pre-mRNA Splicing Is Predominantly Posttranscriptional

Molecular Cell - Tập 24 Số 6 - Trang 917-929 - 2006
Daniel F. Tardiff1, Scott A. Lacadie1, Michael Rosbash1
1Biology Department MS008, Howard Hughes Medical Institute, Brandeis University, 415 South Street , Waltham, Massachusetts 02454

Tóm tắt

Từ khóa


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

Audibert, 2002, In vivo kinetics of mRNA splicing and transport in mammalian cells, Mol. Cell. Biol., 22, 6706, 10.1128/MCB.22.19.6706-6718.2002

Ausubel, 1994

Behzadnia, 2006, Functional spliceosomal A complexes can be assembled in vitro in the absence of a penta-snRNP, RNA, 12, 1738, 10.1261/rna.120606

Bentley, 2005, Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors, Curr. Opin. Cell Biol., 17, 251, 10.1016/j.ceb.2005.04.006

Beyer, 1988, Splice site selection, rate of splicing, and alternative splicing on nascent transcripts, Genes Dev., 2, 754, 10.1101/gad.2.6.754

Brow, 2002, Allosteric cascade of spliceosome activation, Annu. Rev. Genet., 36, 333, 10.1146/annurev.genet.36.043002.091635

Burckin, 2005, Exploring functional relationships between components of the gene expression machinery, Nat. Struct. Mol. Biol., 12, 175, 10.1038/nsmb891

Burge, 1999, Splicing of precursors to mRNAs by the spliceosome, 525

Clark, 2002, Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays, Science, 296, 907, 10.1126/science.1069415

Cramer, 1999, Coupling of transcription with alternative splicing: RNA pol II promoters modulate SF2/ASF and 9G8 effects on an exonic splicing enhancer, Mol. Cell, 4, 251, 10.1016/S1097-2765(00)80372-X

Das, 2006, Functional coupling of RNAP II transcription to spliceosome assembly, Genes Dev., 20, 1100, 10.1101/gad.1397406

David, 2006, A high-resolution map of transcription in the yeast genome, Proc. Natl. Acad. Sci. USA, 103, 5320, 10.1073/pnas.0601091103

de la Mata, 2006, RNA polymerase II C-terminal domain mediates regulation of alternative splicing by SRp20, Nat. Struct. Mol. Biol., 13, 973, 10.1038/nsmb1155

Fong, 2001, Capping, splicing, and 3′ processing are independently stimulated by RNA polymerase II: different functions for different segments of the CTD, Genes Dev., 15, 1783, 10.1101/gad.889101

Furger, 2002, Promoter proximal splice sites enhance transcription, Genes Dev., 16, 2792, 10.1101/gad.983602

Ghosh, 2000, Coupled in vitro synthesis and splicing of RNA polymerase II transcripts, RNA, 6, 1325, 10.1017/S1355838200992537

Goguel, 1993, Splice site choice and splicing efficiency are positively influenced by intramolecular base pairing in yeast, Cell, 72, 893, 10.1016/0092-8674(93)90578-E

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

Guthrie, 1991, Guide to yeast genetics and molecular biology, Methods Enzymol., 194, 389

Hicks, 2006, Linking splicing to Pol II transcription stabilizes pre-mRNAs and influences splicing patterns, PLoS Biol., 4, e147, 10.1371/journal.pbio.0040147

Holstege, 1998, Dissecting the regulatory circuitry of a eukaryotic genome, Cell, 95, 717, 10.1016/S0092-8674(00)81641-4

Howe, 2003, Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae, RNA, 9, 993, 10.1261/rna.5390803

Hyman, 1991, Point mutations upstream of the yeast ADH2 poly(A) site significantly reduce the efficiency of 3′-end formation, Mol. Cell. Biol., 11, 2004, 10.1128/MCB.11.4.2004

Juneau, 2006, Introns regulate RNA and protein abundance in yeast, Genetics, 174, 511, 10.1534/genetics.106.058560

Jurica, 2003, Pre-mRNA splicing: awash in a sea of proteins, Mol. Cell, 12, 5, 10.1016/S1097-2765(03)00270-3

Kadener, 2001, Antagonistic effects of T-Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing, EMBO J., 20, 5759, 10.1093/emboj/20.20.5759

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

Kiseleva, 1994, Assembly and disassembly of spliceosomes along a specific pre-messenger RNP fiber, EMBO J., 13, 6052, 10.1002/j.1460-2075.1994.tb06952.x

Komarnitsky, 2000, Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription, Genes Dev., 14, 2452, 10.1101/gad.824700

Kornblihtt, 2004, Multiple links between transcription and splicing, RNA, 10, 1489, 10.1261/rna.7100104

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

Kyburz, 2006, Direct interactions between subunits of CPSF and the U2 snRNP contribute to the coupling of pre-mRNA 3′ end processing and splicing, Mol. Cell, 23, 195, 10.1016/j.molcel.2006.05.037

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 cotranscriptional splicing is sensitive to transcription elongation mutants, Genes Dev., 20, 2055, 10.1101/gad.1434706

Licatalosi, 2002, Functional interaction of yeast pre-mRNA 3′ end processing factors with RNA polymerase II, Mol. Cell, 9, 1101, 10.1016/S1097-2765(02)00518-X

Listerman, 2006, Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells, Nat. Struct. Mol. Biol., 13, 815, 10.1038/nsmb1135

Lopez, 2001, Uncoupling yeast intron recognition from transcription with recursive splicing, EMBO Rep., 1, 1

Maniatis, 2002, An extensive network of coupling among gene expression machines, Nature, 416, 499, 10.1038/416499a

McCracken, 1997, The C-terminal domain of RNA polymerase II couples mRNA processing to transcription, Nature, 385, 357, 10.1038/385357a0

Mockler, 2005, Applications of DNA tiling arrays for whole-genome analysis, Genomics, 85, 1, 10.1016/j.ygeno.2004.10.005

Morris, 2000, The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II, J. Biol. Chem., 275, 39935, 10.1074/jbc.M004118200

Neugebauer, 2002, On the importance of being co-transcriptional, J. Cell Sci., 115, 3865, 10.1242/jcs.00073

Newman, 1987, Specific accessory sequences in Saccharomyces cerevisiae introns control assembly of pre-mRNAs into spliceosomes, EMBO J., 6, 3833, 10.1002/j.1460-2075.1987.tb02720.x

Parker, 1987, Architecture of fungal introns: implications for spliceosome assembly, 133

Phatnani, 2004, Expanding the functional repertoire of CTD kinase I and RNA polymerase II: novel phosphoCTD-associating proteins in the yeast proteome, Biochemistry, 43, 15702, 10.1021/bi048364h

Pikielny, 1986, Specific small nuclear RNAs are associated with yeast spliceosomes, Cell, 45, 869, 10.1016/0092-8674(86)90561-1

Proudfoot, 2002, Integrating mRNA processing with transcription, Cell, 108, 501, 10.1016/S0092-8674(02)00617-7

Ren, 2000, Genome-wide location and function of DNA binding proteins, Science, 290, 2306, 10.1126/science.290.5500.2306

Stevens, 2002, Composition and functional characterization of the yeast spliceosomal penta-snRNP, Mol. Cell, 9, 31, 10.1016/S1097-2765(02)00436-7

Swinburne, 2006, Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription, Genome Res., 16, 912, 10.1101/gr.5211806

Tardiff, 2006, Arrested yeast splicing complexes indicate stepwise snRNP recruitment during in vivo spliceosome assembly, RNA, 12, 968, 10.1261/rna.50506

Teem, 1983, Expression of a β-galactosidase gene containing the ribosomal protein 51 intron is sensitive to the rna2 mutation of yeast, Proc. Natl. Acad. Sci. USA, 80, 4403, 10.1073/pnas.80.14.4403

Villa, 2002, Spliceosomal snRNAs: Mg(2+)-dependent chemistry at the catalytic core?, Cell, 109, 149, 10.1016/S0092-8674(02)00726-2

Warner, 1999, The economics of ribosome biosynthesis in yeast, Trends Biochem. Sci., 24, 437, 10.1016/S0968-0004(99)01460-7

Wetterberg, 2001, In situ transcription and splicing in the Balbiani ring 3 gene, EMBO J., 20, 2564, 10.1093/emboj/20.10.2564

Wiesner, 2002, Solution structure and ligand recognition of the WW domain pair of the yeast splicing factor Prp40, J. Mol. Biol., 324, 807, 10.1016/S0022-2836(02)01145-2