Mammalian PRP4 Kinase Copurifies and Interacts with Components of Both the U5 snRNP and the N-CoR Deacetylase Complexes

REFERENCES

• Aasland, R., A. F. Stewart, and T. Gibson. 1996. The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB. Trends Biochem. Sci. 21: 87–88.
   PubMed Web of Science ®Google Scholar
• Alahari, S. K., H. Schmidt, and N. F. Kaufer. 1993. The fission yeast prp4+ gene involved in pre-mRNA splicing codes for a predicted serine/threonine kinase and is essential for growth. Nucleic Acids Res. 21: 4079–4083.
   PubMedGoogle Scholar
• Andrews, N. C., and D. V. Faller. 1991. A rapid micropreparation technique for extraction of DNA-binding proteins from limiting numbers of mammalian cells. Nucleic Acids Res. 19: 2499.
   PubMed Web of Science ®Google Scholar
• Bauren, G., and L. Wieslander. 1994. Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell 76: 183–192.
   PubMed Web of Science ®Google Scholar
• Brandner, J. M., S. Reidenbach, C. Kuhn, and W. W. Franke. 1998. Identification and characterization of a novel kind of nuclear protein occurring free in the nucleoplasm and in ribonucleoprotein structures of the “speckle” type. Eur. J. Cell Biol. 75: 295–308.
   PubMedGoogle Scholar
• Caceres, J. F., T. Misteli, G. R. Screaton, D. L. Spector, and A. R. Krainer. 1997. Role of the modular domains of SR proteins in subnuclear localization and alternative splicing specificity. J. Cell Biol. 138: 225–238.
   PubMed Web of Science ®Google Scholar
• Chen, J. D., and R. M. Evans. 1995. A transcriptional co-repressor that interacts with nuclear hormone receptors. Nature 377: 454–457.
   PubMed Web of Science ®Google Scholar
• Chiba, H., M. Muramatsu, A. Nomoto, and H. Kato. 1994. Two human homologues of Saccharomyces cerevisiae SWI2/SNF2 and Drosophila brahma are transcriptional coactivators cooperating with the estrogen receptor and the retinoic acid receptor. Nucleic Acids Res. 22: 1815–1820.
   PubMed Web of Science ®Google Scholar
• Cramer, P., J. F. Caceres, D. Cazalla, S. Kadener, A. F. Muro, F. E. Baralle, and A. R. Kornblihtt. 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: 251–258.
   PubMed Web of Science ®Google Scholar
• Cramer, P., C. G. Pesce, F. E. Baralle, and A. R. Kornblihtt. 1997. Functional association between promoter structure and transcript alternative splicing. Proc. Natl. Acad. Sci. USA 94: 11456–11460.
   PubMed Web of Science ®Google Scholar
• Dignam, J. D., P. L. Martin, B. S. Shastry, and R. G. Roeder. 1983. Eukaryotic gene transcription with purified components. Methods Enzymol. 101: 582–598.
   PubMed Web of Science ®Google Scholar
• Dingwall, A. K., S. J. Beek, C. M. McCallum, J. W. Tamkun, G. V. Kalpana, S. P. Goff, and M. P. Scott. 1995. The Drosophila Snr1 and Brm proteins are related to yeast SWI/SNF proteins and are components of a large protein complex. Mol. Biol. Cell 6: 777–791.
   PubMedGoogle Scholar
• Fong, Y. W., and Q. Zhou. 2001. Stimulatory effect of splicing factors on transcriptional elongation. Nature 414: 929–933.
   PubMed Web of Science ®Google Scholar
• Fry, C. J., and C. L. Peterson. 2001. Chromatin remodeling enzymes: who's on first? Curr. Biol. 11: R185–R197.
   PubMed Web of Science ®Google Scholar
• Ge, H., Y. Si, and A. P. Wolffe. 1998. A novel transcriptional coactivator, p52, functionally interacts with the essential splicing factor ASF/SF2. Mol. Cell 2: 751–759.
   PubMedGoogle Scholar
• Graveley, B. R. 2000. Sorting out the complexity of SR protein functions. RNA 6: 1197–1211.
   PubMed Web of Science ®Google Scholar
• Gross, T., M. Lutzelberger, H. Weigmann, A. Klingenhoff, S. Shenoy, and N. F. Kaufer. 1997. Functional analysis of the fission yeast Prp4 protein kinase involved in pre-mRNA splicing and isolation of a putative mammalian homologue. Nucleic Acids Res. 25: 1028–1035.
   PubMedGoogle Scholar
• Guenther, M. G., O. Barak, and M. A. Lazar. 2001. The SMRT and N-CoR corepressors are activating cofactors for histone deacetylase 3. Mol. Cell. Biol. 21: 6091–6101.
   PubMed Web of Science ®Google Scholar
• Hassig, C. A., T. C. Fleischer, A. N. Billin, S. L. Schreiber, and D. E. Ayer. 1997. Histone deacetylase activity is required for full transcriptional repression by mSin3A. Cell 89: 341–347.
   PubMed Web of Science ®Google Scholar
• Hedley, M. L., H. Amrein, and T. Maniatis. 1995. An amino acid sequence motif sufficient for subnuclear localization of an arginine/serine-rich splicing factor. Proc. Natl. Acad. Sci. USA 92: 11524–11528.
   PubMedGoogle Scholar
• Heinzel, T., R. M. Lavinsky, T. M. Mullen, M. Soderstrom, C. D. Laherty, J. Torchia, W. M. Yang, G. Brard, S. D. Ngo, J. R. Davie, E. Seto, R. N. Eisenman, D. W. Rose, C. K. Glass, and M. G. Rosenfeld. 1997. A complex containing N-CoR, mSin3 and histone deacetylase mediates transcriptional repression. Nature 387: 43–48.
   PubMed Web of Science ®Google Scholar
• Hirose, Y., and J. L. Manley. 2000. RNA polymerase II and the integration of nuclear events. Genes Dev. 14: 1415–1429.
   PubMed Web of Science ®Google Scholar
• Horlein, A. J., A. M. Naar, T. Heinzel, J. Torchia, B. Gloss, R. Kurokawa, A. Ryan, Y. Kamei, M. Soderstrom, and C. K. Glass. 1995. Ligand-independent repression by the thyroid hormone receptor mediated by a nuclear receptor co-repressor. Nature 377: 397–404.
   PubMed Web of Science ®Google Scholar
• Hsieh, J. J., S. Zhou, L. Chen, D. B. Young, and S. D. Hayward. 1999. CIR, a corepressor linking the DNA binding factor CBF1 to the histone deacetylase complex. Proc. Natl. Acad. Sci. USA 96: 23–28.
   PubMed Web of Science ®Google Scholar
• Huang, Y., T. Deng, and B. W. Winston. 2000. Characterization of hPRP4 kinase activation: potential role in signaling. Biochem. Biophys. Res. Commun. 271: 456–463.
   PubMedGoogle Scholar
• Humphrey, G. W., Y. Wang, V. R. Russanova, T. Hirai, J. Qin, Y. Nakatani, and B. H. Howard. 2001. Stable histone deacetylase complexes distinguished by the presence of SANT domain proteins CoREST/kiaa0071 and Mta-L1. J. Biol. Chem. 276: 6817–6824.
   PubMed Web of Science ®Google Scholar
• Jepsen, K., and M. G. Rosenfeld. 2002. Biological roles and mechanistic actions of co-repressor complexes. J. Cell Sci. 115: 689–698.
   PubMed Web of Science ®Google Scholar
• Juan, L. J., W. J. Shia, M. H. Chen, W. M. Yang, E. Seto, Y. S. Lin, and C. W. Wu. 2000. Histone deacetylases specifically downregulate p53-dependent gene activation. J. Biol. Chem. 275: 20436–20443.
   PubMed Web of Science ®Google Scholar
• Kao, H. Y., M. Downes, P. Ordentlich, and R. M. Evans. 2000. Isolation of a novel histone deacetylase reveals that class I and class II deacetylases promote SMRT-mediated repression. Genes Dev. 14: 55–66.
   PubMed Web of Science ®Google Scholar
• Kojima, T., T. Zama, K. Wada, H. Onogi, and M. Hagiwara. 2001. Cloning of human PRP4 reveals interaction with Clk1. J. Biol. Chem. 276: 32247–32256.
   PubMedGoogle Scholar
• Laggerbauer, B., J. Lauber, and R. Luhrmann. 1996. Identification of an RNA-dependent ATPase activity in mammalian U5 snRNPs. Nucleic Acids Res. 24: 868–875.
   PubMedGoogle Scholar
• Lai, M. C., B. H. Teh, and W. Y. Tarn. 1999. A human papillomavirus E2 transcriptional activator: the interactions with cellular splicing factors and potential function in pre-mRNA processing. J. Biol. Chem. 274: 11832–11841.
   PubMedGoogle Scholar
• Lauber, J., G. Plessel, S. Prehn, C. L. Will, P. Fabrizio, K. Groning, W. S. Lane, and R. Luhrmann. 1997. The human U4/U6 snRNP contains 60 and 90kD proteins that are structurally homologous to the yeast splicing factors Prp4p and Prp3p. RNA 3: 926–941.
   PubMedGoogle Scholar
• Le Douarin, B., A. L. Nielsen, J. M. Garnier, H. Ichinose, F. Jeanmougin, R. Losson, and P. Chambon. 1996. A possible involvement of TIF1α and TIF1β in the epigenetic control of transcription by nuclear receptors. EMBO J. 15: 6701–6715.
   PubMed Web of Science ®Google Scholar
• Lee, S. B., and D. A. Haber. 2001. Wilms tumor and the WT1 gene. Exp. Cell Res. 264: 74–99.
   PubMed Web of Science ®Google Scholar
• Li, H., and P. M. Bingham. 1991. Arginine/serine-rich domains of the su(wa) and tra RNA processing regulators target proteins to a subnuclear compartment implicated in splicing. Cell 67: 335–342.
   PubMedGoogle Scholar
• Longman, D., I. L. Johnstone, and J. F. Caceres. 2000. Functional characterization of SR and SR-related genes in Caenorhabditis elegans. EMBO J. 19: 1625–1637.
   PubMedGoogle Scholar
• Makarov, E. M., O. V. Makarova, T. Achsel, and R. Luhrmann. 2000. The human homologue of the yeast splicing factor Prp6p contains multiple TPR elements and is stably associated with the U5 snRNP via protein-protein interactions. J. Mol. Biol. 298: 567–575.
   PubMed Web of Science ®Google Scholar
• Martinez, E., V. B. Palhan, A. Tjernberg, E. S. Lymar, A. M. Gamper, T. K. Kundu, B. T. Chait, and R. G. Roeder. 2001. Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo. Mol. Cell. Biol. 21: 6782–6795.
   PubMed Web of Science ®Google Scholar
• Mathur, M., P. W. Tucker, and H. H. Samuels. 2001. PSF is a novel corepressor that mediates its effect through Sin3A and the DNA binding domain of nuclear hormone receptors. Mol. Cell. Biol. 21: 2298–2311.
   PubMedGoogle Scholar
• Mintz, P. J., S. D. Patterson, A. F. Neuwald, C. S. Spahr, and D. L. Spector. 1999. Purification and biochemical characterization of interchromatin granule clusters. EMBO J. 18: 4308–4320.
   PubMedGoogle Scholar
• Monsalve, M., Z. Wu, G. Adelmant, P. Puigserver, M. Fan, and B. M. Spiegelman. 2000. Direct coupling of transcription and mRNA processing through the thermogenic coactivator PGC-1. Mol. Cell 6: 307–316.
   PubMed Web of Science ®Google Scholar
• Muchardt, C., and M. Yaniv. 1993. A human homologue of Saccharomyces cerevisiae SNF2/SWI2 and Drosophila brm genes potentiates transcriptional activation by the glucocorticoid receptor. EMBO J. 12: 4279–4290.
   PubMed Web of Science ®Google Scholar
• Muchardt, C., and M. Yaniv. 1999. ATP-dependent chromatin remodeling: SWI/SNF and Co. are on the job. J. Mol. Biol. 293: 187–198.
   PubMed Web of Science ®Google Scholar
• Neish, A. S., S. F. Anderson, B. P. Schlegel, W. Wei, and J. D. Parvin. 1998. Factors associated with the mammalian RNA polymerase II holoenzyme. Nucleic Acids Res. 26: 847–853.
   PubMedGoogle Scholar
• Neubauer, G., A. King, J. Rappsilber, C. Calvio, M. Watson, P. Ajuh, J. Sleeman, A. Lamond, and M. Mann. 1998. Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nat. Genet. 20: 46–50.
   PubMed Web of Science ®Google Scholar
• Nishikimi, A., J. Mukai, N. Kioka, and M. Yamada. 1999. A novel mammalian nuclear protein similar to Schizosaccharomyces pombe Prp1p/Zer1p and Saccharomyces cerevisiae Prp6p pre-mRNA splicing factors. Biochim. Biophys. Acta 1435: 147–152.
   PubMedGoogle Scholar
• Ouyang, P., and S. P. Sugrue. 1996. Characterization of pinin, a novel protein associated with the desmosome-intermediate filament complex. J. Cell Biol. 135: 1027–1042.
   PubMedGoogle Scholar
• Pflum, M. K., J. K. Tong, W. S. Lane, and S. L. Schreiber. 2001. Histone deacetylase I phosphorylation promotes enzymatic activity and complex formation. J. Biol. Chem. 276: 47733–47741.
   PubMed Web of Science ®Google Scholar
• Sarkissian, M., A. Winne, and R. Lafyatis. 1996. The mammalian homolog of suppressor-of-white-apricot regulates alternative mRNA splicing of CD45 exon 4 and fibronectin IIICS. J. Biol. Chem. 271: 31106–31114.
   PubMedGoogle Scholar
• Schwelnus, W., K. Richert, F. Opitz, T. Gross, Y. Habara, T. Tani, and N. F. Kaufer. 2001. Fission yeast Prp4p kinase regulates pre-mRNA splicing by phosphorylating a non-SR-splicing factor. EMBO Rep. 2: 35–41.
   PubMedGoogle Scholar
• Simons, A., C. Melamed-Bessudo, R. Wolkowicz, J. Sperling, R. Sperling, L. Eisenbach, and V. Rotter. 1997. PACT: cloning and characterization of a cellular p53 binding protein that interacts with Rb. Oncogene 14: 145–155.
   PubMedGoogle Scholar
• Spector, D. L., X. D. Fu, and T. Maniatis. 1991. Associations between distinct pre-mRNA splicing components and the cell nucleus. EMBO J. 10: 3467–3481.
   PubMed Web of Science ®Google Scholar
• Stojdl, D. F., and J. C. Bell. 1999. SR protein kinases: the splice of life. Biochem. Cell Biol. 77: 293–298.
   PubMed Web of Science ®Google Scholar
• Sutherland, H. G., G. K. Mumford, K. Newton, L. V. Ford, R. Farrall, G. Dellaire, J. F. Caceres, and W. A. Bickmore. 2001. Large-scale identification of mammalian proteins localized to nuclear sub-compartments. Hum. Mol. Genet. 10: 1995–2011.
   PubMed Web of Science ®Google Scholar
• Tate, P., M. Lee, S. Tweedie, W. C. Skarnes, and W. A. Bickmore. 1998. Capturing novel mouse genes encoding chromosomal and other nuclear proteins. J. Cell Sci. 111(Pt. 17): 2575–2585.
   PubMedGoogle Scholar
• Underhill, C., M. S. Qutob, S. P. Yee, and J. Torchia. 2000. 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.
   PubMedGoogle Scholar
• Will, C. L., B. Kastner, and R. Luhrmann. 1994. Analysis of ribonucleoprotein interactions, p. 141–177. In D. Rickwood and B. D. Hames (ed.), RNA processing: practical approach. IRL Press, Oxford, England.
   Google Scholar
• Wilson, C. J., D. M. Chao, A. N. Imbalzano, G. R. Schnitzler, R. E. Kingston, and R. A. Young. 1996. RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell 84: 235–244.
   PubMed Web of Science ®Google Scholar
• Woppmann, A., C. L. Will, U. Kornstadt, P. Zuo, J. L. Manley, and R. Luhrmann. 1993. Identification of an snRNP-associated kinase activity that phosphorylates arginine/serine rich domains typical of splicing factors. Nucleic Acids Res. 21: 2815–2822.
   PubMedGoogle Scholar
• Wu, J., and M. Grunstein. 2000. 25 years after the nucleosome model: chromatin modifications. Trends Biochem. Sci. 25: 619–623.
   PubMed Web of Science ®Google Scholar
• Yang, L., L. J. Embree, S. Tsai, and D. D. Hickstein. 1998. Oncoprotein TLS interacts with serine-arginine proteins involved in RNA splicing. J. Biol. Chem. 273: 27761–27764.
   PubMed Web of Science ®Google Scholar
• Yao, Y. L., Yang, W. M., and E. Seto. 2001. Regulation of transcription factor YY1 by acetylation and deacetylation. Mol. Cell. Biol. 21: 5979–5991.
   PubMed Web of Science ®Google Scholar
• You, A., J. K. Tong, C. M. Grozinger, and S. L. Schreiber. 2001. CoREST is an integral component of the CoREST-human histone deacetylase complex. Proc. Natl. Acad. Sci. USA 98: 1454–1458.
   PubMed Web of Science ®Google Scholar
• Zachar, Z., T. B. Chou, J. Kramer, I. P. Mims, and P. M. Bingham. 1994. Analysis of autoregulation at the level of pre-mRNA splicing of the suppressor-of-white-apricot gene in Drosophila. Genetics 137: 139–150.
   PubMedGoogle Scholar
• Zhou, S., M. Fujimuro, J. J. Hsieh, L. Chen, and S. D. Hayward. 2000. A role for SKIP in EBNA2 activation of CBF1-repressed promoters. J. Virol. 74: 1939–1947.
   PubMedGoogle Scholar