Human Transcription Elongation Factor CA150 Localizes to Splicing Factor-Rich Nuclear Speckles and Assembles Transcription and Splicing Components into Complexes through Its Amino and Carboxyl Regions

REFERENCES

• Bedford, M. T., and P. Leder. 1999. The FF domain: a novel motif that often accompanies WW domains. Trends Biochem. Sci. 24:264–265.
   PubMedGoogle 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
• Bohne, J., S. E. Cole, C. Suñe, B. R. Lindman, V. D. Ko, T. F. Vogt, and M. A. Garcia-Blanco. 2000. Expression analysis and mapping of the mouse and human transcriptional regulator CA150. Mamm. Genome 11:390–393.
   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, S. van der Zee, 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
• Carty, S. M., A. C. Goldstrohm, C. Suñe, M. A. Garcia-Blanco, and A. L. Greenleaf. 2000. Protein-interaction modules that organize nuclear function: FF domains of CA150 bind the phosphoCTD of RNA polymerase II. Proc. Natl. Acad. Sci. USA 97:9015–9020.
   PubMed Web of Science ®Google Scholar
• Carty, S. M., and A. L. Greenleaf. 2002. Hyperphosphorylated C-terminal repeat domain-associating proteins in the nuclear proteome link transcription to DNA/chromatin modification and DNA processing. Mol. Cell. Proteomics 1:598–610.
   PubMed Web of Science ®Google Scholar
• Cho, E. J., C. R. Rodriguez, T. Tagaki, and S. Buratowski. 1998. Allosteric interactions between capping enzyme subunits and the RNA polymerase II carboxy-terminal domain. Genes Dev. 15:3482–3487.
   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. 15:3319–3326.
   Google Scholar
• Cmarko, D. 1999. Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjection. Mol. Biol. Cell 10:211–223.
   PubMed Web of Science ®Google Scholar
• Corden, J. L. 1990. Tails of RNA polymerase II. Trends Biochem. Sci. 15:383–387.
   PubMed Web of Science ®Google Scholar
• Dignam, J. D., R. N. Lebovitz, and R. G. Roeder. 1983. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11:1475–1489.
   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
• Feaver, W. J., O. Gileadi, Y. Li, and R. D. Kornberg. 1991. CTD kinase associated with yeast RNA polymerase II initiation factor b. Cell 67:1223–1230.
   PubMed Web of Science ®Google Scholar
• Fisher, P. A., L. Lin, M. McConnell, A. Greenleaf, J. M. Lee, and D. E. Smith. 1989. Heat shock-induced appearance of RNA polymerase II in karyoskeletal protein-enriched (nuclear “matrix”) fractions correlates with transcriptional shutdown in Drosophila melanogaster. J. Biol. Chem. 264:3464–3469.
   PubMed Web of Science ®Google Scholar
• Ghosh, S., and M. A. Garcia-Blanco. 2000. Coupled in vitro synthesis and splicing of RNA polymerase II transcripts. RNA 9:1325–1334.
   Google Scholar
• Goldstrohm, A. C., A. L. Greenleaf, and M. A. Garcia-Blanco. 2001. Co-transcriptional splicing of pre-messenger RNAs: consideration for the mechanism of alternative splicing. Gene 277:31–47.
   PubMed Web of Science ®Google Scholar
• Goldstrohm, A. C., T. R. Albrecht, C. Suñe, M. T. Bedford, and M. A. Garcia-Blanco. 2001. The transcription elongation factor CA150 interacts with RNA polymerase II and the pre-mRNA splicing factor SF1. Mol. Cell. Biol. 21:7617–7628.
   PubMed Web of Science ®Google Scholar
• Greenleaf, A. L. 1993. Positive patches and negative noodles: linking RNA processing to transcription? Trends Biochem. Sci. 18:117–119.
   PubMed Web of Science ®Google Scholar
• Guth, S., and J. Valcarcel. 2000. Kinetic role for mammalian SF1/BBP in spliceosome assembly and function after polypyrimidine tract recognition by U2AF. J. Biol. Chem. 275:38059–38066.
   PubMed Web of Science ®Google Scholar
• Harlow, E., and D. Lane. 1999. Using antibodies: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Herrmann, C. H., and M. A. Mancini. 2001. The CDK9 and cyclin T subunits of TAK/P-TEFb localize to splicing factor-rich nuclear speckle regions. J. Cell Sci. 114:1491–1503.
   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
• Hirose, Y., R. Tacke, and J. L. Manley. 1999. Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. Genes Dev. 13:1234–1239.
   PubMed Web of Science ®Google Scholar
• Ho, C. K., and S. Shuman. 1999. Distinct roles for CTD Ser-2 and Ser-5 phosphorylation in the recruitment and allosteric activation of mammalian mRNA capping enzyme. Mol. Cell 3:405–411.
   PubMed Web of Science ®Google Scholar
• Kadener, S., P. Cramer, G. Nogues, D. Cazalla, M. Mata, J. P. Fededa, S. E. Werbajh, A. Srebrow, and A. R. Kornblihtt. 2001. Antagonistic effects of T-Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing. EMBO J. 20:5759–5768.
   PubMed Web of Science ®Google Scholar
• Kameoka, S., P. Duque, and M. M. Konarska. 2004. p54(nrb) associates with the 5′ splice site within large transcription/splicing complexes. EMBO J. 23:1782–1791.
   PubMedGoogle Scholar
• Kato, H., H. Sumimoto, P. Pognonec, C. H. Chen, C. A. Rosen, and R. G. Roeder. 1992. HIV-1 Tat acts as a processivity factor in vitro in conjunction with cellular elongation factors. Genes Dev. 6:655–666.
   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
• Komarnitsky, P., E. J. Cho, and S. Buratowski. 2000. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14:2452–2460.
   PubMed Web of Science ®Google Scholar
• Kornblihtt, A. R., M. de la Mata, J. P. Fededa, M. J. Muñoz, and G. Nogues. 2004. Multiple links between transcription and splicing. RNA 10:1489–1498.
   PubMed Web of Science ®Google Scholar
• Lamond, A. I., and D. L. Spector. 1993. Nuclear speckles: a model for nuclear organelles. Nat. Rev. Mol. Cell Biol. 4:605–612.
   Google Scholar
• Li, X. Y., and M. R. Green. 1998. The HIV-1 Tat cellular coactivator Tat-SF1 is a general transcription elongation factor. Genes Dev. 12:2992–2996.
   PubMedGoogle Scholar
• Lin, K. T., R. M. Lu, and W. Y. Tarn. 2004. The WW domain-containing proteins interact with the early spliceosome and participate in pre-mRNA splicing in vivo. Mol. Cell. Biol. 24:9176–9185.
   PubMedGoogle Scholar
• Lu, H., L. Zawel, L. Fisher, J. M. Egly, and D. Reinberg. 1992. Human general transcription factor IIH phosphorylates the C-terminal domain of RNA polymerase II. Nature 358:641–645.
   PubMed Web of Science ®Google Scholar
• Mancebo, H. G. L., J. Flygare, J. Tomassini, P. Luu, Y. Zhu, C. Blau, D. Hazuda, D. Price, and O. Flores. 1997. P-TEFb kinase is required for HIV Tat transcriptional activation in vivo and in vitro. Genes Dev. 11:2633–2644.
   PubMed Web of Science ®Google Scholar
• Marshall, N. F., and D. H. Price. 1995. Purification of P-TEFb, a transcription factor required for the transition into productive elongation. J. Biol. Chem. 270:12335–12338.
   PubMed Web of Science ®Google Scholar
• Marshall, N. F., J. 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
• 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
• McCracken, S., N. Fong, E. Rosonina, K. Yankulov, G. Brothers, D. Siderovski, A. Hessel, S. Foster, 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. 15:3306–3318.
   Google Scholar
• Miller, C. R., S. F. Jamison, and M. A. Garcia-Blanco. 1997. HeLa nuclear extract: a modified protocol. Academic Press, New York, N.Y.
   Google 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
• Misteli, T., and D. L. Spector. 1999. RNA polymerase II targets pre-mRNA splicing factors to transcription sites in vivo. Mol. Cell 3:697–705.
   PubMed Web of Science ®Google Scholar
• Misteli, T., J. F. Caceres, J. D. Clement, A. R. Krainer, M. F. Wilkinson, and D. L. Spector. 1998. Serine phosphorylation of SR proteins is required for their recruitment to sites of transcription in vivo. J. Cell Biol. 143:297–307.
   PubMed Web of Science ®Google Scholar
• Mizushima, S., and S. Nagata. 1990. pEF-BOS, a powerful mammalian expression vector. Nucleic Acids Res. 18:5322.
   PubMed Web of Science ®Google Scholar
• Morris, D. P., and A. L. Greenleaf. 2000. The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II. J. Biol. Chem. 275:39935–39943.
   PubMed Web of Science ®Google Scholar
• Mortillaro, M. J., B. J. Blencowe, X. 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
• Myers, J. K., D. P. Morris, A. L. Greenleaf, and T. G. Oas. 2001. Phosphorylation of RNA polymerase II CTD fragments results in tight binding to the WW domain from the yeast prolyl isomerase Ess1. Biochemistry 40:8479–8486.
   PubMed Web of Science ®Google 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
• O'Keefe, R. T., A. Mayeda, C. L. Sadowski, A. R. Krainer, and D. L. Spector. 1994. Disruption of pre-mRNA splicing in vivo results in reorganization of splicing factors. J. Cell Biol. 124:249–260.
   PubMed Web of Science ®Google Scholar
• Orphanides, G., and D. Reinberg. 2002. A unified theory of gene expression. Cell 108:439–451.
   PubMed Web of Science ®Google Scholar
• Patturajan, M., X. Wei, R. Berezney, and J. L. Corden. 1998. A nuclear matrix protein interacts with the phosphorylated C-terminal domain of RNA polymerase II. Mol. Cell. Biol. 18:2406–2415.
   PubMed Web of Science ®Google Scholar
• Phair, R. D., and T. Misteli. 2000. High mobility of proteins in the mammalian cell nucleus. Nature 404:604–609.
   PubMed Web of Science ®Google Scholar
• Proudfoot, N. J., A. Furger, and M. J. Dye. 2002. Integrating mRNA processing with transcription. Cell 108:501–512.
   PubMed Web of Science ®Google Scholar
• Rain, J. C., Z. Rafi, Z. Rhani, P. Legrain, and A. Kramer. 1998. Conservation of functional domains involved in RNA binding and protein-protein interactions in human and Saccharomyces cerevisiae pre-mRNA splicing factor SF1. RNA 4:551–565.
   PubMedGoogle Scholar
• Roberts, G. C., C. Gooding, H. Y. Mak, N. J. Proudfoot, and C. W. Smith. 1998. Co-transcriptional commitment to alternative splice site selection. Nucleic Acids Res. 26:5568–5572.
   PubMed Web of Science ®Google Scholar
• Robson-Dixon, N. D., and M. A. Garcia-Blanco. 2004. MAZ elements alter transcription elongation and silencing of the fibroblast growth factor receptor 2 exon IIIb. J. Biol. Chem. 279:29075–29084.
   PubMedGoogle Scholar
• Saitoh, N., C. S. Spahr, S. D. Patterson, P. Bubulya, A. F. Neuwald, and D. L. Spector. 2004. Proteomic analysis of interchromatin granule clusters. Mol. Biol. Cell 15:3876–3890.
   PubMed Web of Science ®Google Scholar
• Selenko, P., G. Gregorovic, R. Sprangers, G. Stier, Z. Rhani, A. Kramer, and M. Sattler. 2003. Structural basis for the molecular recognition between human splicing factors U2AF65 and SF1/mBBP. Mol. Cell 4:965–976.
   Google Scholar
• Smith, K. P., P. T. Moen, K. L. Wydner, J. R. Coleman, and J. B. Lawrence. 1999. Processing of endogenous pre-mRNAs in association with SC-35 domains is gene specific. J. Cell Biol. 144:617–629.
   PubMedGoogle Scholar
• Smith, M. J., S. Kulkarni, and T. Pawson. 2004. FF domains of CA150 bind transcription and splicing factors through multiple weak interactions. Mol. Cell. Biol. 24:9274–9285.
   PubMedGoogle Scholar
• Spector, D. L. 1993. Macromolecular domains within the cell nucleus. Annu. Rev. Cell Biol. 9:265–315.
   PubMedGoogle Scholar
• Spector, D. L. 1993. Nuclear domains. J. Cell Sci. 114:2891–2893.
   Google Scholar
• Spector, D. L., W. H. Schrier, and H. Busch. 1983. Immunoelectron microscopic localization of snRNPs. Biol. Cell 49:1–10.
   PubMed Web of Science ®Google Scholar
• Suñe, C., A. C. Goldstrohm, J. Peng, D. H. Price, and M. A. Garcia-Blanco. 2000. An in vitro transcription system that recapitulates equine infectious anemia virus Tat-mediated inhibition of human immunodeficiency virus type 1 Tat activity demonstrates a role for positive transcription elongation factor b and associated proteins in the mechanism of Tat activation. Virology 274:356–366.
   PubMedGoogle Scholar
• Suñé, C., and M. A. Garcia-Blanco. 1999. Transcriptional cofactor CA150 regulates RNA polymerase II elongation in a TATA-box-dependent manner. Mol. Cell. Biol. 19:4719–4728.
   PubMedGoogle Scholar
• Suñé, C., R. Hayashi, Y. Liu, W. S. Lane, R. A. Young, and M. A. Garcia-Blanco. 1997. CA150, a nuclear protein associated with the RNA polymerase II holoenzyme, is involved in Tat-activated human immunodeficiency virus type 1 transcription. Mol. Cell. Biol. 17:6029–6039.
   PubMedGoogle Scholar
• Wei, X., S. Somanathan, J. Samarabandu, and R. Berezney. 1999. Three-dimensional visualization of transcription sites and their association with splicing factor-rich nuclear speckles. J. Cell Biol. 146:543–558.
   PubMedGoogle Scholar
• Yan, D., R. Perriman, H. Igel, K. J. Howe, M. Neville, and M. Ares, Jr. 1998. CUS2, a yeast homolog of human Tat-SF1, rescues function of misfolded U2 through an unusual RNA recognition motif. Mol. Cell. Biol. 16:818–828.
   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
• Zeng, C., and S. M. Berget. 2000. Participation of the C-terminal domain of RNA polymerase II in exon definition during pre-mRNA splicing. Mol. Cell. Biol. 20:8290–8301.
   PubMed Web of Science ®Google Scholar
• Zhou, Q., and P. A. Sharp. 1996. Tat-SF1: cofactor for stimulation of transcription elongation by HIV-1 Tat. Science 274:605–610.
   PubMedGoogle Scholar
• Zhou, Q., D. Chen, E. Pierstorff, and K. Luo. 1998. Transcription elongation factor P-TEFb mediates Tat activation of HIV-1 transcription at multiple stages. EMBO J. 17:3681–3691.
   PubMed Web of Science ®Google Scholar
• Zhou, Q., and P. A. Sharp. 1995. Novel mechanism and factor for regulation by HIV-1 Tat. EMBO J. 14:321–328.
   PubMedGoogle Scholar
• Zhou, Z., L. J. Licklider, S. P. Gygi, and R. Reed. 2002. Comprehensive proteomic analysis of the human spliceosome. Nature 419:182–185.
   PubMed Web of Science ®Google Scholar
• Zhu, Y., T. Pe'ery, J. Peng, Y. Ramanathan, N. Marshall, T. Marshall, B. Amendt, M. Mathews, and D. Price. 1997. Transcription elongation factor P-TEFb is required for HIV-1 Tat transactivation in vitro. Genes Dev. 11:2622–2632.
   PubMed Web of Science ®Google Scholar