A Nuclear Matrix Protein Interacts with the Phosphorylated C-Terminal Domain of RNA Polymerase II

REFERENCES

• Akhtar, A., G. Faye, and D. L. Bentley 1996. Distinct activated and non-activated RNA polymerase II complexes in yeast. EMBO J. 15: 4654–4664.
   PubMedGoogle Scholar
• Allison, L. A., M. Moyle, M. Shales, and C. J. Ingles 1985. Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases. Cell 42: 599–610.
   PubMed Web of Science ®Google Scholar
• Allison, L. A., J. K.-C. Wong, V. D. Fitzpatrick, M. Moyle, and C. J. Ingles 1988. The C-terminal domain of the largest subunit of RNA polymerase II of Saccharomyces cerevisiae, Drosophila melanogaster, and mammals: a conserved structure with an essential function. Mol. Cell. Biol. 8: 321–329.
   PubMed Web of Science ®Google Scholar
• Bartolomei, M. S., N. F. Halden, C. R. Cullen, and J. L. Corden 1988. Genetic analysis of the repetitive carboxyl-terminal domain of the largest subunit of mouse RNA polymerase II. Mol. Cell. Biol. 8: 330–339.
   PubMed Web of Science ®Google Scholar
• Baskaran, R., M. E. Dahmus, and J. Y. Wang 1993. Tyrosine phosphorylation of mammalian RNA polymerase II carboxyl-terminal domain. Proc. Natl. Acad. Sci. USA 90: 11167–11171.
   PubMed Web of Science ®Google Scholar
• Basler, J., N. D. Hastie, D. Pietras, S. I. Matsui, A. A. Sandberg, and R. Berezney 1981. Hybridization of nuclear matrix attached deoxyribonucleic acid fragments. Biochemistry 20: 6921–6929.
   PubMedGoogle Scholar
• Bauren, G., W. Q. Jiang, K. Bernholm, F. Gu, and L. Wieslander 1996. Demonstration of a dynamic, transcription-dependent organization of pre-mRNA splicing factors in polytene nuclei. J. Cell Biol. 133: 929–941.
   PubMedGoogle 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
• Belgrader, P., A. J. Siegel, and R. Berezney 1991. A comprehensive study on the isolation and characterization of the HeLa S3 nuclear matrix. J. Cell Sci. 98: 281–291.
   PubMedGoogle Scholar
• Berezney, R., and D. S. Coffey 1974. Identification of a nuclear protein matrix. Biochem. Biophys. Res. Commun. 60: 1410–1417.
   PubMed Web of Science ®Google Scholar
• Berezney, R., and D. S. Coffey 1977. Nuclear matrix. Isolation and characterization of a framework structure from rat liver nuclei. J. Cell Biol. 73: 616–637.
   PubMed Web of Science ®Google Scholar
• Berezney, R., M. Mortillaro, H. Ma, C. Meng, J. Samarabandu, X. Wei, S. Somanathan, W. S. Liou, S. J. Pan, and P. C. Cheng 1996. Connecting nuclear architecture and genomic function. J. Cell. Biochem. 62: 223–226.
   PubMed Web of Science ®Google Scholar
• Berezney, R., M. J. Mortillaro, H. Ma, X. Wei, and J. Samarabandu 1995. The nuclear matrix: a structural milieu for genomic function. Int. Rev. Cytol. 162A: 1–65.
   PubMedGoogle Scholar
• Beyer, A. L., and Y. N. Osheim 1988. Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes Dev. 2: 754–765.
   PubMed Web of Science ®Google Scholar
• Blencowe, B. J., R. Issner, J. Kim, P. McCaw, and P. A. Sharp 1995. New proteins related to the Ser-Arg family of splicing factors. RNA 1: 852–865.
   PubMedGoogle Scholar
• Blencowe, B. J., J. A. Nickerson, R. Issner, S. Penman, and P. A. Sharp 1994. Association of nuclear matrix antigens with exon-containing splicing complexes. J. Cell Biol. 127: 593–607.
   PubMed Web of Science ®Google Scholar
• Bourquin, J. P., I. Stagljar, P. Meier, P. Moosmann, J. Silke, T. Baechi, O. Georgiev, and W. Schaffner 1997. A serine/arginine-rich nuclear matrix cyclophilin interacts with the C-terminal domain of RNA polymerase II. Nucleic Acids Res. 25: 2055–2061.
   PubMed Web of Science ®Google Scholar
• Bregman, D. B., L. Du, Y. Li, S. Ribisi, and S. L. Warren 1994. Cytostellin distributes to nuclear regions enriched with splicing factors. J. Cell Sci. 107: 387–396.
   PubMedGoogle Scholar
• Bregman, D. B., L. Du, S. Vanderzee, and S. L. Warren 1995. Transcription-dependent redistribution of the large subunit of RNA polymerase II to discrete nuclear domains. J. Cell Biol. 129: 287–298.
   PubMedGoogle Scholar
• Chabot, B., S. Bisotto, and M. Vincent 1995. The nuclear matrix phosphoprotein p255 associates with splicing complexes as part of the [U4/U6.U5] tri-snRNP particle. Nucleic Acids Res. 23: 3206–3213.
   PubMed Web of Science ®Google Scholar
• Cho, E. J., T. Takagi, C. R. Moore, and S. Buratowski 1997. mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev. 11: 3319–3326.
   PubMed Web of Science ®Google Scholar
• Corden, J. L., and C. J. Ingles Carboxy-terminal domain of the largest subunit of eukaryotic RNA polymerase II Transcriptional regulation In: McKnight, S. L., and K. R. Yamamoto1199281–108Cold Spring Harbor Laboratory Press, Plainview, N.Y.
   Google Scholar
• Corden, J. L. 1990. Tails of RNA polymerase II. Trends Biochem. Sci. 15: 383–387.
   PubMed Web of Science ®Google Scholar
• Corden, J. L., D. L. Cadena, Ahearn J., Jr., and M. E. Dahmus 1985. A unique structure at the carboxyl terminus of the largest subunit of eukaryotic RNA polymerase II. Proc. Natl. Acad. Sci. USA 82: 7934–7938.
   PubMed Web of Science ®Google Scholar
• Corden, J. L., and M. Patturajan 1997. A CTD function linking transcription to splicing. Trends Biochem. Sci. 22: 413–416.
   PubMedGoogle Scholar
• Dahmus, M. E. 1995. Phosphorylation of the C-terminal domain of RNA polymerase II. Biochim. Biophys. Acta 1261: 171–182.
   PubMedGoogle Scholar
• Dahmus, M. E. 1996. Reversible phosphorylation of the C-terminal domain of RNA polymerase II. J. Biol. Chem. 271: 19009–19012.
   PubMed Web of Science ®Google Scholar
• Dantonel, J. C., K. G. Murthy, J. L. Manley, and L. Tora 1997. Transcription factor TFIID recruits factor CPSF for formation of 3′ end of mRNA. Nature 389: 399–402.
   PubMed Web of Science ®Google Scholar
• Desai, D., Y. Gu, and D. O. Morgan 1992. Activation of human cyclin-dependent kinases in vitro. Mol. Biol. Cell 3: 571–582.
   PubMed Web of Science ®Google Scholar
• Du, L., and S. L. Warren 1997. A functional interaction between the carboxy-terminal domain of RNA polymerase II and pre-mRNA splicing. J. Cell Biol. 136: 5–18.
   PubMed Web of Science ®Google Scholar
• Egyhazi, E., A. Ossoinak, A. Pigon, C. Holmgren, J. M. Lee, and A. L. Greenleaf 1996. Phosphorylation dependence of the initiation of productive transcription of Balbiani ring 2 genes in living cells. Chromosoma 104: 422–433.
   PubMedGoogle Scholar
• Fay, F. S., K. L. Taneja, S. Shenoy, L. Lifshitz, and R. H. Singer 1997. Quantitative digital analysis of diffuse and concentrated nuclear distributions of nascent transcripts, SC35 and poly(A). Exp. Cell Res. 231: 27–37.
   PubMed Web of Science ®Google Scholar
• Fu, X. D. 1995. The superfamily of arginine/serine-rich splicing factors. RNA 1: 663–680.
   PubMed Web of Science ®Google Scholar
• Fu, X. D., and T. Maniatis 1990. Factor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus. Nature 343: 437–441.
   PubMed Web of Science ®Google Scholar
• Gebara, M. M., M. H. Sayre, and J. L. Corden 1997. Phosphorylation of the carboxy-terminal repeat domain in RNA polymerase II by cyclin-dependent kinases is sufficient to inhibit transcription. J. Cell. Biochem. 64: 390–402.
   PubMedGoogle Scholar
• Grande, M. A., I. Vanderkraan, L. Dejong, and R. Vandriel 1997. Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II. J. Cell Sci. 110: 1781–1791.
   PubMed Web of Science ®Google Scholar
• Gunnery, S., and M. B. Mathews 1995. Functional mRNA can be generated by RNA polymerase III. Mol. Cell. Biol. 15: 3597–3607.
   PubMedGoogle Scholar
• He, D. C., T. Martin, and S. Penman 1991. Localization of heterogeneous nuclear ribonucleoprotein in the interphase nuclear matrix core filaments and on perichromosomal filaments at mitosis. Proc. Natl. Acad. Sci. USA 88: 7469–7473.
   PubMedGoogle Scholar
• Iborra, F. J., A. Pombo, D. A. Jackson, and P. R. Cook 1996. Active RNA polymerases are localized within discrete transcription “factories” in human nuclei. J. Cell Sci. 109: 1427–1436.
   PubMed Web of Science ®Google Scholar
• Jackson, D. A., and P. R. Cook 1985. Transcription occurs at a nucleoskeleton. EMBO J. 4: 919–925.
   PubMed Web of Science ®Google Scholar
• Jackson, D. A., A. B. Hassan, R. J. Errington, and P. R. Cook 1993. Visualization of focal sites of transcription within human nuclei. EMBO J. 12: 1059–1065.
   PubMed Web of Science ®Google Scholar
• Kim, E., L. Du, D. B. Bregman, and S. L. Warren 1997. Splicing factors associate with hyperphosphorylated RNA polymerase II in the absence of pre-mRNA. J. Cell Biol. 136: 19–28.
   PubMed Web of Science ®Google Scholar
• LeMaire, M. F., and C. S. Thummel 1990. Splicing precedes polyadenylation during Drosophila E74A transcription. Mol. Cell. Biol. 10: 6059–6063.
   PubMedGoogle Scholar
• Marshall, N. F., J. M. Peng, Z. Xie, and D. H. Price 1996. Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase. J. Biol. Chem. 271: 27176–27183.
   PubMed Web of Science ®Google Scholar
• Mattaj, I. W. 1994. RNA processing—splicing in space. Nature 372: 727–728.
   PubMedGoogle Scholar
• McCracken, S., N. Fong, E. Rosonina, K. Yankulov, G. Brothers, D. Siderovski, A. Hessel, S. Foster, A. E. Program, S. Shuman, and D. L. Bentley 1997. 5′-capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II. Genes Dev. 11: 3306–3318.
   PubMed Web of Science ®Google Scholar
• McCracken, S., N. Fong, K. Yankulov, S. Ballantyne, G. Pan, J. Greenblatt, S. D. Patterson, M. Wickens, and D. L. Bentley 1997. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385: 357–361.
   PubMed Web of Science ®Google Scholar
• Misteli, T., J. F. Caceres, and D. L. Spector 1997. The dynamics of a pre-mRNA splicing factor in living cells. Nature 387: 523–527.
   PubMed Web of Science ®Google Scholar
• Mortillaro, M. J., B. J. Blencowe, X. Y. Wei, H. Nakayasu, L. Du, S. L. Warren, P. A. Sharp, and R. Berezney 1996. A hyperphosphorylated form of the large subunit of RNA polymerase II is associated with splicing complexes and the nuclear matrix. Proc. Natl. Acad. Sci. USA 93: 8253–8257.
   PubMed Web of Science ®Google Scholar
• Nakayasu, H., and R. Berezney 1989. Mapping replicational sites in the eucaryotic cell nucleus. J. Cell Biol. 108: 1–11.
   PubMed Web of Science ®Google Scholar
• Nakayasu, H., and R. Berezney 1991. Nuclear matrins: identification of the major nuclear matrix proteins. Proc. Natl. Acad. Sci. USA 88: 10312–10316.
   PubMedGoogle Scholar
• Neugebauer, K. M., and M. B. Roth 1997. Distribution of pre-mRNA splicing factors at sites of RNA polymerase II transcription. Genes Dev. 11: 1148–1159.
   PubMed Web of Science ®Google Scholar
• Neugebauer, K. M., and M. B. Roth 1997. Transcription units as RNA processing units. Genes Dev. 11: 3279–3285.
   PubMedGoogle Scholar
• Nickerson, J. A., B. J. Blencowe, and S. Penman 1995. The architectural organization of nuclear metabolism. Int. Rev. Cytol. 162A: 67–123.
   PubMedGoogle Scholar
• Nonet, M., D. Sweetser, and R. A. Young 1987. Functional redundancy and structural polymorphism in the large subunit of RNA polymerase II. Cell 50: 909–915.
   PubMedGoogle Scholar
• O’Brien, T., S. Hardin, A. Greenleaf, and J. T. Lis 1994. Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation. Nature 370: 75–77.
   PubMed Web of Science ®Google Scholar
• Patturajan, M., and J. L. Corden. Unpublished observations.
   Google Scholar
• Patturajan, M., R. J. Schulte, B. M. Sefton, R. Berezney, M. Vincent, O. Bensaude, S. L. Warren, and J. L. Corden 1997. Growth-related changes in phosphorylation of yeast RNA polymerase II. J. Biol. Chem. 273: 4689–4694.
   Google Scholar
• Shuman, S. 1997. Origins of mRNA identity-capping enzymes bind to the phosphorylated C-terminal domain of RNA polymerase II. Proc. Natl. Acad. Sci. USA 94: 12758–12760.
   PubMedGoogle Scholar
• Singer, R. H., and M. R. Green 1997. Compartmentalization of eukaryotic gene expression—causes and effects. Cell 91: 291–294.
   PubMedGoogle Scholar
• Sisodia, S. S., B. Sollner-Webb, and D. W. Cleveland 1987. Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation. Mol. Cell. Biol. 7: 3602–3612.
   PubMed Web of Science ®Google Scholar
• Smale, S. T., and R. Tjian 1985. Transcription of herpes simplex virus tk sequences under the control of wild-type and mutant human RNA polymerase I promoters. Mol. Cell. Biol. 5: 352–362.
   PubMed Web of Science ®Google Scholar
• Spector, D. L. 1993. Macromolecular domains within the cell nucleus. Annu. Rev. Cell Biol. 9: 265–315.
   PubMedGoogle Scholar
• Steinmetz, E. J. 1997. Pre-mRNA processing and the CTD of RNA polymerase II: the tail that wags the dog? Cell 89: 491–494.
   PubMedGoogle Scholar
• Tanner, S., I. Stagljar, O. Georgiev, W. Schaffner, and J. P. Bourquin 1997. A novel SR-related protein specifically interacts with the carboxyl-terminal domain (CTD) of RNA polymerase II through a conserved interaction domain. Biol. Chem. 378: 565–571.
   PubMedGoogle Scholar
• Thompson, N. E., T. H. Steinberg, D. B. Aronson, and R. R. Burgess 1989. Inhibition of in vivo and in vitro transcription by monoclonal antibodies prepared against wheat germ RNA polymerase II that react with the heptapeptide repeat of eukaryotic RNA polymerase II. J. Biol. Chem. 264: 11511–11520.
   PubMedGoogle Scholar
• Vincent, M., P. Lauriault, M. F. Dubois, S. Lavoie, O. Bensaude, and B. Chabot 1996. The nuclear matrix protein p255 is a highly phosphorylated form of RNA polymerase II largest subunit which associates with spliceosomes. Nucleic Acids Res. 24: 4649–4652.
   PubMedGoogle Scholar
• Vogelstein, B., and B. F. Hunt 1982. A subset of small nuclear ribonucleoprotein particle antigens is a component of the nuclear matrix. Biochem. Biophys. Res. Commun. 105: 1224–1232.
   PubMedGoogle Scholar
• Wansink, D. G., W. Schul, I. van der Kraan, B. van Steensel, R. van Driel, and L. de Jong 1993. Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus. J. Cell Biol. 122: 283–293.
   PubMed Web of Science ®Google Scholar
• Weeks, J. R., S. E. Hardin, J. Shen, J. M. Lee, and A. L. Greenleaf 1993. Locus-specific variation in phosphorylation state of RNA polymerase II in vivo: correlations with gene activity and transcript processing. Genes Dev. 7: 2329–2344.
   PubMedGoogle Scholar
• West, M. L., and J. L. Corden 1995. Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutants. Genetics 140: 1223–1233.
   PubMed Web of Science ®Google Scholar
• Wu, J. Y., and T. Maniatis 1993. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell 75: 1061–1070.
   PubMed Web of Science ®Google Scholar
• Xing, Y., C. V. Johnson, Moen P. T., Jr., J. A. McNeil, and J. Lawrence 1995. Nonrandom gene organization: structural arrangements of specific pre-mRNA transcription and splicing with SC-35 domains. J. Cell Biol. 131: 1635–1647.
   PubMedGoogle Scholar
• Yue, Z. Y., E. Maldonado, R. Pillutla, H. Cho, D. Reinberg, and A. J. Shatkin 1997. Mammalian capping enzyme complements mutant Saccharomyces cerevisiae lacking mRNA guanylyltransferase and selectively binds the elongating form of RNA polymerase II. Proc. Natl. Acad. Sci. USA 94: 12898–12903.
   PubMed Web of Science ®Google Scholar
• Yuryev, A., M. Patturajan, Y. Litingtung, R. V. Joshi, C. Gentile, M. Gebara, and J. L. Corden 1996. The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc. Natl. Acad. Sci. USA 93: 6975–6980.
   PubMed Web of Science ®Google Scholar
• Zehring, W. A., J. M. Lee, J. R. Weeks, R. S. Jokerst, and A. L. Greenleaf 1988. The C-terminal repeat domain of RNA polymerase II largest subunit is essential in vivo but is not required for accurate transcription initiation in vitro. Proc. Natl. Acad. Sci. USA 85: 3698–3702.
   PubMedGoogle Scholar
• Zeitlin, S., A. Parent, S. Silverstein, and A. Efstratiadis 1987. Pre-mRNA splicing and the nuclear matrix. Mol. Cell. Biol. 7: 111–120.
   PubMed Web of Science ®Google Scholar
• Zeitlin, S., R. C. Wilson, and A. Efstratiadis 1989. Autonomous splicing and complementation of in vivo-assembled spliceosomes. J. Cell Biol. 108: 765–777.
   PubMed Web of Science ®Google Scholar
• Zeng, C., E. Kim, S. L. Warren, and S. M. Berget 1997. Dynamic relocation of transcription and splicing factors dependent upon transcriptional activity. EMBO J. 16: 1401–1412.
   PubMedGoogle Scholar
• Zhang, G., K. L. Taneja, R. H. Singer, and M. R. Green 1994. Localization of pre-mRNA splicing in mammalian nuclei. Nature 372: 809–812.
   PubMed Web of Science ®Google Scholar
• Zhang, J., and J. L. Corden 1991. Identification of phosphorylation sites in the repetitive carboxyl-terminal domain of the mouse RNA polymerase II largest subunit. J. Biol. Chem. 266: 2290–2296.
   PubMedGoogle Scholar