The human SWI/SNF subunit Brm is a regulator of alternative splicing

Nature Structural and Molecular Biology

Volumn 13, Issue 1, 2006, Pages 22-29

  Batsché, Eric ^a   Yaniv, Moshe ^a   Muchardt, Christian ^a  

^a INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BIM PROTEIN; CYCLIN D1; HERMES ANTIGEN; MESSENGER RNA; PROTEIN; PROTEIN BRM; PROTEIN SAM68; PROTEIN SUBUNIT; PROTEIN SWI; RNA POLYMERASE II; TRANSCRIPTION FACTOR SNF; UNCLASSIFIED DRUG; UVOMORULIN;

ALTERNATIVE RNA SPLICING; ARTICLE; CATALYST; CHROMATIN ASSEMBLY AND DISASSEMBLY; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME PHOSPHORYLATION; EXON; FUNCTIONAL PROTEOMICS; GENETIC CODE; GENETIC REGULATION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FUNCTION; RNA PROCESSING; RNA TRANSCRIPTION; SPLICEOSOME;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; ALTERNATIVE SPLICING; ANTIGENS, CD44; CELL LINE, TUMOR; DNA-BINDING PROTEINS; EXONS; HUMANS; PHOSPHOPROTEINS; PHOSPHORYLATION; PROTEIN BINDING; PROTEIN SUBUNITS; RNA POLYMERASE II; RNA, SMALL NUCLEAR; RNA-BINDING PROTEINS; TRANSCRIPTION FACTORS;

EID: 30044441988     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb1030     Document Type: Article

References (50)

1. Sharp, P.A. The discovery of split genes and RNA splicing. Trends Biochem. Sci. 30, 279-281 (2005).
2. Matlin, A.J., Clark, F. & Smith, C.W. Understanding alternative splicing: towards a cellular code. Nat. Rev. Mol. Cell Biol. 6, 386-398 (2005).
3. Shin, C. & Manley, J.L. Cell signalling and the control of pre-mRNA splicing. Nat. Rev. Mol. Cell Biol. 5, 727-738 (2004).
4. Konig, H., Ponta, H. & Herrlich, P. Coupling of signal transduction to alternative pre-mRNA splicing by a composite splice regulator. EMBO J. 17, 2904-2913 (1998).
5. Matter, N., Herrlich, P. & Konig, H. Signal-dependent regulation of splicing via phosphorylation of Sam68. Nature 420, 691-695 (2002).
6. Lukong, K.E. & Richard, S. Sam68, the KH domain-containing superSTAR. Biochim. Biophys. Acta 1653, 73-86 (2003).
7. Stoss, O. et al. p59(fyn)-mediated phosphorylation regulates the activity of the tissue-specific splicing factor rSLM-1. Mol. Cell. Neurosci. 27, 8-21 (2004).
8. Grossman, J.S. et al. The use of antibodies to the polypyrimidine tract binding protein (PTB) to analyze the protein components that assemble on alternatively spliced pre-mRNAs that use distant branch points. RNA 4, 613-625 (1998).
9. Kornblihtt, A.R. Promoter usage and alternative splicing. Curr. Opin. Cell Biol. 17, 262-268 (2005).
10. Auboeuf, D. et al. Differential recruitment of nuclear receptor coactivators may determine alternative RNA splice site choice in target genes. Proc. Natl. Acad. Sci. USA 101, 2270-2274 (2004).
11. Auboeuf, D., Honig, A., Berget, S.M. & O'Malley, B.W. Coordinate regulation of transcription and splicing by steroid receptor coregulators. Science 298, 416-419 (2002).
12. Masuhiro, Y. et al. Splicing potentiation by growth factor signals via estrogen receptor phosphorylation. Proc. Natl. Acad. Sci. USA 102, 8126-8131 (2005).
13. Rosonina, E., Bakowski, M.A., McCracken, S. & Blencowe, B.J. Transcriptional activators control splicing and 3′-end cleavage levels. J. Biol. Chem. 278, 43034-43040 (2003).
14. Martens, J.A. & Winston, F. Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Curr. Opin. Genet. Dev. 13, 136-142 (2003).
15. Reisman, D.N. et al. Concomitant down-regulation of BRM and BRG1 in human tumor cell lines: differential effects on RB-mediated growth arrest vs CD44 expression. Oncogene 21, 1196-1207 (2002).
16. Kadam, S. & Emerson, B.M. Transcriptional specificity of human SWI/SNF BRG1 and BRM chromatin remodeling complexes. Mol. Cell 11, 377-389 (2003).
17. Marshall, T.W., Link, K.A., Petre-Draviam, C.E. & Knudsen, K.E. Differential requirement of SWI/SNF for androgen receptor activity. J. Biol. Chem. 278, 30605-30613 (2003).
18. Sullivan, E.K., Weirich, C.S., Guyon, J.R., Sif, S. & Kingston, R.E. Transcriptional activation domains of human heat shock factor 1 recruit human SWI/SNF. Mol. Cell. Biol. 21, 5826-5837 (2001).
19. Corey, L.L., Weirich, C.S., Benjamin, I.J. & Kingston, R.E. Localized recruitment of a chromatin-remodeling activity by an activator in vivo drives transcriptional elongation. Genes Dev. 17, 1392-1401 (2003).
20. Wilson, C.J. et al. RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell 84, 235-244 (1996).
21. Neish, A.S., Anderson, S.F., Schlegel, B.P., Wei, W. & Parvin, J.D. Factors associated with the mammalian RNA polymerase II holoenzyme. Nucleic Acids Res. 26, 847-853 (1998).
22. Underhill, C., Qutob, M.S., Yee, S.P. & Torchia, J. A novel nuclear receptor corepressor complex, N-CoR, contains components of the mammalian SWI/SNF complex and the corepressor KAP-1. J. Biol. Chem. 275, 40463-40470 (2000).
23. Dellaire, G. et al. Mammalian PRP4 kinase copurifies and interacts with components of both the U5 snRNP and the N-CoR deacetylase complexes. Mol. Cell. Biol. 22, 5141-5156 (2002).
24. Banine, F. et al. SWI/SNF chromatin-remodeling factors induce changes in DNA methylation to promote transcriptional activation. Cancer Res. 65, 3542-3547 (2005).
25. Fukudome, Y., Yanagihara, K., Takeichi, M., Ito, F. & Shibamoto, S. Characterization of a mutant E-cadherin protein encoded by a mutant gene frequently seen in diffuse-type human gastric carcinoma. Int. J. Cancer 88, 579-583 (2000).
26. U, M., Miyashita, T., Shikama, Y., Tadokoro, K. & Yamada, M. Molecular cloning and characterization of six novel isoforms of human Bim, a member of the proapoptotic Bcl-2 family. FEBS Lett. 509, 135-141 (2001).
27. Lu, F., Gladden, A.B. & Diehl, J.A. An alternatively spliced cyclin D1 isoform, cyclin D1b, is a nuclear oncogene. Cancer Res. 63, 7056-7061 (2003).
28. Goodison, S., Urquidi, V. & Tarin, D. CD44 cell adhesion molecules. Mol. Pathol. 52, 189-196 (1999).
29. Reyes, J.C. et al. Altered control of cellular proliferation in the absence of mammalian brahma (SNF2α). EMBO J. 17, 6979-6991 (1998).
30. Bourachot, B., Yaniv, M. & Muchardt, C. The activity of mammalian brm/SNF2α is dependent on a high-mobility- group protein I/Y-like DNA binding domain. Mol. Cell. Biol. 19, 3931-3939 (1999).
31. Kouskouti, A. & Talianidis, I. Histone modifications defining active genes persist after transcriptional and mitotic inactivation. EMBO J. 24, 347-357 (2005).
32. Jones, J.C. et al. C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats. J. Biol. Chem. 279, 24957-24964 (2004).
33. de la Mata, M. et al. A slow RNA polymerase II affects alternative splicing in vivo. Mol. Cell 12, 525-532 (2003).
34. Howe, K.J., Kane, C.M. & Ares, M., Jr. Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. RNA 9, 993-1006 (2003).
35. Roberts, G.C., Gooding, C., Mak, H.Y., Proudfoot, N.J. & Smith, C.W. Co-transcriptional commitment to alternative splice site selection. Nucleic Acids Res. 26, 5568-5572 (1998).
36. Boehm, A.K., Saunders, A., Werner, J. & Lis, J.T. Transcription factor and polymerase recruitment, modification, and movement on dhsp70 in vivo in the minutes following heat shock. Mol. Cell. Biol. 23, 7628-7637 (2003).
37. Morris, D.P., Michelotti, G.A. & Schwinn, D.A. Evidence that phosphorylation of the RNA polymerase II carboxyl-terminal repeats is similar in yeast and humans. J. Biol. Chem. 280, 31368-31377 (2005).
38. Cheng, C. & Sharp, P.A. RNA polymerase II accumulation in the promoter-proximal region of the dihydrofolate reductase and γ-actin genes. Mol. Cell. Biol. 23, 1961-1967 (2003).
39. Cho, H. et al. A human RNA polymerase II complex containing factors that modify chromatin structure. Mol. Cell. Biol. 18, 5355-5363 (1998).
40. Cereghini, S. & Yaniv, M. Assembly of transfected DNA into chromatin: structural changes in the origin-promoter-enhancer region upon replication. EMBO J. 3, 1243-1253 (1984).
41. Soutoglou, E. & Talianidis, I. Coordination of PIC assembly and chromatin remodeling during differentiation-induced gene activation. Science 295, 1901-1904 (2002).
42. Agalioti, T., Chen, G. & Thanos, D. Deciphering the transcriptional histone acetylation code for a human gene. Cell 111, 381-392 (2002).
43. Muchardt, C., Reyes, J.C., Bourachot, B., Leguoy, E. & Yaniv, M. The hbrm and BRG-1 proteins, components of the human SNF/SWI complex, are phosphorylated and excluded from the condensed chromosomes during mitosis. EMBO J. 15, 3394-3402 (1996).
44. Sims, R.J., III., Belotserkovskaya, R. & Reinberg, D. Elongation by RNA polymerase II: the short and long of it. Genes Dev. 18, 2437-2468 (2004).
45. Trautinger, B.W., Jaktaji, R.P., Rusakova, E. & Lloyd, R.G. RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription. Mol. Cell 19, 247-258 (2005).
46. Bourachot, B., Yaniv, M. & Muchardt, C. Growth inhibition by the mammalian SWI-SNF subunit Brm is regulated by acetylation. EMBO J. 22, 6505-6515 (2003).
47. Batsché, E., Moschopoulos, P., Desroches, J., Bilodeau, S. & Drouin, J. Retinoblastoma and the related pocket protein p107 act as coactivators of NeuroD1 to enhance gene transcription. J. Biol. Chem. 280, 16088-16095 (2005).
48. Muchardt, C., Bourachot, B., Reyes, J.C. & Yaniv, M. ras transformation is associated with decreased expression of the brm/SNF2α ATPase from the mammalian SWI-SNF complex. EMBO J. 17, 223-231 (1998).
49. Muchardt, C., Sardet, C., Bourachot, B., Onufryk, C. & Yaniv, M. A human protein with homology to Saccharomyces cerevisiae SNF5 interacts with the potential helicase hbrm. Nucleic Acids Res. 23, 1127-1132 (1995).
50. Pfaffl, M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29, 2002-2007 (2001).