Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5′ss base pairing in yeast

Molecular Cell

Volumn 19, Issue 1, 2005, Pages 65-75

  Lacadie, Scott A ^a   Rosbash, Michael ^a  

^a BRANDEIS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL NUCLEAR RIBONUCLEOPROTEIN; SMALL NUCLEAR RNA;

ARTICLE; CHROMATIN; DYNAMICS; FUNGAL GENE; GENE MUTATION; IMMUNOPRECIPITATION; INTRON; NONHUMAN; PROTEIN CONFORMATION; PROTEIN FUNCTION; SACCHAROMYCES CEREVISIAE; SPLICEOSOME; YEAST;

BASE PAIRING; BETA-GALACTOSIDASE; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; GENES, FUNGAL; GENES, REPORTER; INTRONS; MODELS, BIOLOGICAL; MUTATION; RNA SPLICING; RNA, SMALL NUCLEAR; SACCHAROMYCES CEREVISIAE; SPLICEOSOMES; TRANSCRIPTION, GENETIC;

EID: 21244469725     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2005.05.006     Document Type: Article

References (71)

1. N. Abovich, and M. Rosbash Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals Cell 89 1997 403 412
2. N. Abovich, X.C. Liao, and M. Rosbash The yeast MUD2 protein: an interaction with PRP11 defines a bridge between commitment complexes and U2 snRNP addition Genes Dev. 8 1994 843 854
3. K.C. Abruzzi, S. Lacadie, and M. Rosbash Biochemical analysis of TREX complex recruitment to intronless and intron-containing yeast genes EMBO J. 23 2004 2620 2631
4. G.J. Anderson, M. Bach, R. Lührmann, and J.D. Beggs Conservation between yeast and man of a protein associated with U5 small nuclear ribonucleoprotein Nature 342 1989 819 821
5. M. Ares Jr., L. Grate, and M.H. Pauling A handful of intron-containing genes produces the lion's share of yeast mRNA RNA 5 1999 1138 1139
6. G. Bauren, and L. Wieslander Splicing of balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription Cell 76 1994 183 192
7. J.A. Berglund, K. Chua, N. Abovich, R. Reed, and M. Rosbash The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC Cell 89 1997 781 787
8. J.A. Berglund, M. Rosbash, and S.C. Schultz Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines RNA 7 2001 682 691
9. A.L. Beyer, and Y.N. Osheim Splice site selection, rate of splicing, and alternative splicing on nascent transcripts Genes Dev. 2 1988 754 765
10. C.B. Burge, T. Tuschl, and P.A. Sharp Splicing of precursors to mRNAs by the spliceosomes R.F. Gesteland T.R. Cech J.F. Atkins The RNA World Second Edition 1999 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY 525 560
11. F. Caspary, and B. Seraphin The yeast U2A′/U2B complex is required for pre-spliceosome formation EMBO J. 17 1998 6348 6358
12. J.Y. Chen, L. Stands, J.P. Staley, R.R. Jackups Jr., L.J. Latus, and T.H. Chang Specific alterations of U1-C protein or U1 small nuclear RNA can eliminate the requirement of Prp28p, an essential DEAD box splicing factor Mol. Cell 7 2001 227 232
13. H.V. Colot, F. Stutz, and M. Rosbash The yeast splicing factor MUD13 is a commitment complex component and corresponds to CBP20, the small subunit of the nuclear cap-binding complex Genes Dev. 10 1996 1699 1708
14. H. Du, and M. Rosbash The U1 snRNP protein U1C recognizes the 5′ splice site in the absence of base pairing Nature 419 2002 86 90
15. H. Du, D.F. Tardiff, M.J. Moore, and M. Rosbash Effects of the U1C L13 mutation and temperature regulation of yeast commitment complex formation Proc. Natl. Acad. Sci. USA 101 2004 14841 14846
16. A. Furger, J.M. O'Sullivan, A. Binnie, B.A. Lee, and N.J. Proudfoot Promoter proximal splice sites enhance transcription Genes Dev. 16 2002 2792 2799
17. V. Galy, O. Gadal, M. Fromont-Racine, A. Romano, A. Jacquier, and U. Nehrbass Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1 Cell 116 2004 63 73
18. Görnemann, J., Kotovic, K.M., Hujer, K., and Neugebauer, K.M. (2005). Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. Mol. Cell 19, this issue, 53-63.
19. L. Guarente, R.R. Yocum, and P. Gifford A GAL10-CYC1 hybrid yeast promoter identifies the GAL4 regulatory region as an upstream site Proc. Natl. Acad. Sci. USA 79 1982 7410 7414
20. C. Guthrie, and G.R. Fink Guide to yeast genetics and molecular biology Methods Enzymol. 194 1991 389 398
21. A. Jacquier, and M. Rosbash RNA splicing and intron turnover are greatly diminished by a mutant yeast branch point Proc. Natl. Acad. Sci. USA 83 1986 5835 5839
22. A. Jacquier, J.R. Rodriguez, and M. Rosbash A quantitative analysis of the effects of 5′ junction and TACTAAC box mutants and mutant combinations on yeast mRNA splicing Cell 43 1985 423 430
23. T.H. Jensen, K. Dower, D. Libri, and M. Rosbash Early formation of mRNP: license for export or quality control? Mol. Cell 11 2003 1129 1138
24. M.S. Jurica, and M.J. Moore Pre-mRNA splicing: awash in a sea of proteins Mol. Cell 12 2003 5 14
25. S. Kandels-Lewis, and B. Séraphin Involvement of U6 snRNA in 5′ splice site selection Science 262 1993 2035 2039
26. E. Kiseleva, T. Wurtz, N. Visa, and B. Daneholt Assembly and disassembly of spliceosomes along a specific pre-messenger RNP fiber EMBO J. 13 1994 6052 6061
27. B.B. Konforti, M.J. Koziolkiewicz, and M.M. Konarska Disruption of base pairing between the 5′ splice site and the 5′ end of U1 snRNA is required for spliceosome assembly Cell 75 1993 863 873
28. A.R. Kornblihtt, M. de la Mata, J.P. Fededa, M.J. Munoz, and G. Nogues Multiple links between transcription and splicing RNA 10 2004 1489 1498
29. K.M. Kotovic, D. Lockshon, L. Boric, and K.M. Neugebauer Cotranscriptional recruitment of the U1 snRNP to intron-containing genes in yeast Mol. Cell. Biol. 23 2003 5768 5779
30. P. Legrain, and M. Rosbash Some cis- and trans-acting mutants for splicing target pre-mRNA to the cytoplasm Cell 57 1989 573 583
31. E.P. Lei, and P.A. Silver Intron status and 3′-end formation control cotranscriptional export of mRNA Genes Dev. 16 2002 2761 2766
32. M.F. LeMaire, and C.S. Thummel Splicing precedes polyadenylation during Drosophila E74A transcription Mol. Cell. Biol. 10 1990 6059 6063
33. C.R. Lesser, and C. Guthrie Mutations in U6 snRNA that alter splice site specificity: implications for the active site Science 262 1993 1982 1988
34. J.D. Lewis, E. Izaurralde, A. Jarmolowski, C. McGuigan, and I.W. Mattaj A nuclear cap-binding complex facilitates association of U1 snRNP with the cap-proximal 5′ splice site Genes Dev. 10 1996 1683 1698
35. X.C. Liao, H.V. Colot, Y. Wang, and M. Rosbash Requirements for U2 snRNP addition to yeast pre-mRNA Nucleic Acids Res. 20 1992 4237 4245
36. D. Libri, N. Graziani, C. Saguez, and J. Boulay Multiple roles for the yeast SUB2/yUAP56 gene in splicing Genes Dev. 15 2001 36 41
37. A.M. MacMillan, C.C. Query, C.R. Allerson, S. Chen, G.L. Verdine, and P.A. Sharp Dynamic association of proteins with the pre-mRNA branch region Genes Dev. 8 1994 3008 3020
38. H.D. Madhani, and C. Guthrie A novel base-pairing interaction between U2 and U6 mRNAs suggests a mechanism for the catalytic activation of the spliceosome Cell 71 1992 803 817
39. P.A. Maroney, C.M. Romfo, and T.W. Nilsen Functional recognition of 5′ splice site by U4/U6.U5 tri-snRNP defines a novel ATP-dependent step in early spliceosome assembly Mol. Cell 6 2000 317 328
40. S. Michaud, and R. Reed An ATP-independent complex commits pre-mRNA to the mammalian spliceosome assembly pathway Genes Dev. 5 1991 2534 2546
41. K.M. Neugebauer On the importance of being co-transcriptional J. Cell Sci. 115 2002 3865 3871
42. A. Newman, and C. Norman Mutations in yeast U5 snRNA alter the specificity of 5′ splice-site cleavage Cell 65 1991 115 123
43. A.J. Newman The role of U5 snRNP in pre-mRNA splicing EMBO J. 16 1997 5797 5800
44. A.J. Newman, and C. Norman U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites Cell 68 1992 743 754
45. R. Parker, P.G. Siliciano, and C. Guthrie Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA Cell 49 1987 229 239
46. E. Pascolo, and B. Séraphin The branchpoint residue is recognized during commitment complex formation before being bulged out of the U2 snRNA-pre-mRNA duplex Mol. Cell. Biol. 17 1997 3469 3476
47. C.W. Pikielny, and M. Rosbash mRNA splicing efficiency in yeast and the contribution of nonconserved sequences Cell 41 1985 119 126
48. O. Puig, A. Gottschalk, P. Fabrizio, and B. Seraphin Interaction of the U1 snRNP with nonconserved intronic sequences affects 5′ splice site selection Genes Dev. 13 1999 569 580
49. C.C. Query, M.J. Moore, and P.A. Sharp Branch nucleophile selection in pre-mRNA splicing: evidence for the bulged duplex model Genes Dev. 8 1994 587 597
50. J.L. Reyes, P. Kois, B.B. Konforti, and M.M. Konarska The canonical GU dinucleotide at the 5′ splice site is recognized by p220 of the U5 snRNP within the spliceosome RNA 2 1996 213 225
51. S.W. Ruby, T.-H. Chang, and J. Abelson Four yeast spliceosomal proteins (PRP5, PRP9, PRP11, and PRP21) interact to promote U2 snRNP binding to pre-mRNA Genes Dev. 7 1993 1909 1925
52. B. Rutz, and B. Seraphin Transient interaction of BBP/ScSF1 and Mud2 with the splicing machinery affects the kinetics of spliceosome assembly RNA 5 1999 1 13
53. B. Rutz, and B. Seraphin A dual role for BBP/ScSF1 in nuclear pre-mRNA retention and splicing EMBO J. 19 2000 1873 1886
54. H. Sawa, and J. Abelson Evidence for a base-pairing interaction between U6 snRNA and the 5′ splice site during the splicing reaction in yeast Proc. Natl. Acad. Sci. USA 89 1992 11269 11273
55. B. Seraphin, and M. Rosbash Identification of functional U1 snRNA-pre-mRNA complexes committed to spliceosome assembly and splicing Cell 59 1989 349 358
56. B. Seraphin, and M. Rosbash The yeast branchpoint sequence is not required for the formation of a stable U1 snRNP-pre-mRNA complex and is recognized in the absence of U2 snRNA EMBO J. 10 1991 1209 1216
57. B. Seraphin, L. Kretzner, and M. Rosbash A U1 snRNA:pre-mRNA base pairing interaction is required early in yeast spliceosome assembly but does not uniquely define the 5′ cleavage site EMBO J. 7 1988 2533 2538
58. M. Spingola, L. Grate, D. Haussler, and M. Ares Jr. Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae RNA 5 1999 221 234
59. J.P. Staley, and C. Guthrie An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p Mol. Cell 3 1999 55 64
60. S.W. Stevens, D.E. Ryan, H.Y. Ge, R.E. Moore, M.K. Young, T.D. Lee, and J. Abelson Composition and functional characterization of the yeast spliceosomal penta-snRNP Mol. Cell 9 2002 31 44
61. J. Tang, N. Abovich, M. Fleming, B. Séraphin, and M. Rosbash Identification and characterization of the yeast homologue of U1 snRNP-specific protein C EMBO J. 16 1997 4082 4091
62. J.L. Teem, and M. Rosbash 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 1983 4403 4407
63. S. Teigelkamp, A.J. Newman, and J.D. Beggs Extensive interactions of PRP8 protein with the 5′ and 3′ splice sites during splicing suggest a role in stabilization of exon alignment by U5 snRNA EMBO J. 14 1995 2602 2612
64. J.G. Umen, and C. Guthrie Prp16p, Slu7p, and Prp8p interact with the 3′ splice site in two distinct stages during the second catalytic step of pre-mRNA splicing RNA 1 1995 584 597
65. T. Villa, J.A. Pleiss, and C. Guthrie Spliceosomal snRNAs: Mg(2+)-dependent chemistry at the catalytic core? Cell 109 2002 149 152
66. D.A. Wassarman, and J.A. Steitz Interactions of small nuclear RNA's with precursor messenger RNA during in vitro splicing Science 257 1992 1918 1925
67. J. Wuarin, and U. Schibler Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing Mol. Cell. Biol. 14 1994 7219 7225
68. J.R. Wyatt, E.J. Sontheimer, and J.A. Steitz Site-specific cross-linking of mammalian U5 snRNP to the 5′ splice site before the first step of pre-mRNA splicing Genes Dev. 6 1992 2542 2553
69. D. Zhang, and M. Rosbash Identification of eight proteins that cross-link to pre-mRNA in the yeast commitment complex Genes Dev. 13 1999 581 592
70. D. Zhang, N. Abovich, and M. Rosbash A biochemical function for the Sm complex Mol. Cell 7 2001 319 329
71. M. Zhang, and M.R. Green Identification and characterization of yUAP/Sub2p, a yeast homolog of the essential human pre-mRNA splicing factor hUAP56 Genes Dev. 15 2001 30 35