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Transcriptional Regulation

Two Cyclin-Dependent Kinases Promote RNA Polymerase II Transcription and Formation of the Scaffold Complex

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Pages 1721-1735 | Received 04 Aug 2003, Accepted 11 Nov 2003, Published online: 27 Mar 2023

REFERENCES

  • Akoulitchev, S., Chuikov S., and Reinberg D.. 2000. TFIIH is negatively regulated by cdk8-containing mediator complexes. Nature 407:102–106.
  • Akoulitchev, S., Makela T., Weinberg R. A., and Reinberg D.. 1995. Requirement for TFIIH kinase activity in transcription by RNA polymerase II. Nature 377:557–560.
  • Balciunas, D., Hallberg M., Bjorklund S., and Ronne H.. 2003. Functional interactions within yeast mediator and evidence of differential subunit modifications. J. Biol. Chem. 278:3831–3839.
  • Bishop, A. C., Buzko O., and Shokat K. M.. 2001. Magic bullets for protein kinases. Trends Cell Biol. 11:167–172.
  • Bishop, A. C., Ubersax J. A., Petsch D. T., Matheos D. P., Gray N. S., Blethrow J., Shimizu E., Tsien J. Z., Schultz P. G., Rose M. D., Wood J. L., Morgan D. O., and Shokat K. M.. 2000. A chemical switch for inhibitor-sensitive alleles of any protein kinase. Nature 407:395–401.
  • Borggrefe, T., Davis R., Erdjument-Bromage H., Tempst P., and Kornberg R. D.. 2002. A complex of the Srb8, -9, -10, and -11 transcriptional regulatory proteins from yeast. J. Biol. Chem. 277:44202–44207.
  • Brachmann, C. B., Davies A., Cost G. J., Caputo E., Li J., Hieter P., and Boeke J. D.. 1998. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14:115–132.
  • Cai, H., and Luse D. S.. 1987. Transcription initiation by RNA polymerase II in vitro. Properties of preinitiation, initiation, and elongation complexes. J. Biol. Chem. 262:298–304.
  • Carlson, M. 1997. Genetics of transcriptional regulation in yeast: connections to the RNA polymerase II CTD. Annu. Rev. Cell Dev. Biol. 13:1–23.
  • Chi, Y., Huddleston M. J., Zhang X., Young R. A., Annan R. S., Carr S. A., and Deshaies R. J.. 2001. Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev. 15:1078–1092.
  • Cho, E. J., Kobor M. S., Kim M., Greenblatt J., and Buratowski S.. 2001. Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain. Genes Dev. 15:3319–3329.
  • Davis, J. A., Takagi Y., Kornberg R. D., and Asturias F. A.. 2002. Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. Mol. Cell 10:409–415.
  • Gelbart, M. E., Rechsteiner T., Richmond T. J., and Tsukiyama T.. 2001. Interactions of Isw2 chromatin remodeling complex with nucleosomal arrays: analyses using recombinant yeast histones and immobilized templates. Mol. Cell. Biol. 21:2098–2106.
  • Hengartner, C. J., Myer V. E., Liao S. M., Wilson C. J., Koh S. S., and Young R. A.. 1998. Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases. Mol. Cell 2:43–53.
  • Hirst, M., Kobor M. S., Kuriakose N., Greenblatt J., and Sadowski I.. 1999. GAL4 is regulated by the RNA polymerase II holoenzyme-associated cyclin-dependent protein kinase SRB10/CDK8. Mol. Cell 3:673–678.
  • Holstege, F. C., Jennings E. G., Wyrick J. J., Lee T. I., Hengartner C. J., Green M. R., Golub T. R., Lander E. S., and Young R. A.. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95:717–728.
  • Jiang, Y., and Gralla J. D.. 1994. RNA polymerase II phosphorylation: uncoupling from GAL4-VP16 directed Open complex formation and transcription in a reconstituted system. Nucleic Acids Res. 22:4958–4962.
  • Jiang, Y., Yan M., and Gralla J. D.. 1996. A three-step pathway of transcription initiation leading to promoter clearance at an activation RNA polymerase II promoter. Mol. Cell. Biol. 16:1614–1621.
  • Jones, E. W. 1991. Tackling the protease problem in Saccharomyces cerevisiae. Methods Enzymol. 194:428–453.
  • Keogh, M. C., Cho E. J., Podolny V., and Buratowski S.. 2002. Kin28 is found within TFIIH and a Kin28-Ccl1-Tfb3 trimer complex with differential sensitivities to T-loop phosphorylation. Mol. Cell. Biol. 22:1288–1297.
  • Komarnitsky, P., Cho E. J., and Buratowski S.. 2000. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14:2452–2460.
  • Kuras, L., and Struhl K.. 1999. Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature 399:609–613.
  • Lee, T. I., and Young R. A.. 2000. Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet. 34:77–137.
  • Liu, Y., Ranish J. A., Aebersold R., and Hahn S.. 2001. Yeast nuclear extract contains two major forms of RNA polymerase II mediator complexes. J. Biol. Chem. 276:7169–7175.
  • Makela, T. P., Parvin J. D., Kim J., Huber L. J., Sharp P. A., and Weinberg R. A.. 1995. A kinase-deficient transcription factor TFIIH is functional in basal and activated transcription. Proc. Natl. Acad. Sci. USA 92:5174–5178.
  • Matangkasombut, O., Buratowski R. M., Swilling N. W., and Buratowski S.. 2000. Bromodomain factor 1 corresponds to a missing piece of yeast TFIID. Genes Dev. 14:951–962.
  • Nelson, C., Goto S., Lund K., Hung W., and Sadowski I.. 2003. Srb10/Cdk8 regulates yeast filamentous growth by phosphorylating the transcription factor Ste12. Nature 421:187–190.
  • Ohkuma, Y., and Roeder R. G.. 1994. Regulation of TFIIH ATPase and kinase activities by TFIIE during active initiation complex formation. Nature 368:160–163.
  • Orphanides, G., Lagrange T., and Reinberg D.. 1996. The general transcription factors of RNA polymerase II. Genes Dev. 10:2657–2683.
  • Orphanides, G., and Reinberg D.. 2002. A unified theory of gene expression. Cell 108:439–451.
  • Polson, A. G., Huang L., Lukac D. M., Blethrow J. D., Morgan D. O., Burlingame A. L., and Ganem D.. 2001. Kaposi's sarcoma-associated herpesvirus K-bZIP protein is phosphorylated by cyclin-dependent kinases. J. Virol. 75:3175–3184.
  • Prelich, G. 2002. RNA polymerase II carboxy-terminal domain kinases: emerging clues to their function. Eukaryot. Cell 1:153–162.
  • Ranish, J. A., Yi E. C., Leslie D. M., Purvine S. O., Goodlett D. R., Eng J., and Aebersold R.. 2003. The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 33:349–355.
  • Ranish, J. A., Yudkovsky N., and Hahn S.. 1999. Intermediates in formation and activity of the RNA polymerase II preinitiation complex: holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB. Genes Dev. 13:49–63.
  • Reeves, W. M., and Hahn S.. 2003. Activator-independent functions of the yeast mediator sin4 complex in preinitiation complex formation and transcription reinitiation. Mol. Cell. Biol. 23:349–358.
  • Rigaut, G., Shevchenko A., Rutz B., Wilm M., Mann M., and Seraphin B.. 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17:1030–1032.
  • Rossignol, M., Kolb-Cheynel I., and Egly J. M.. 1997. Substrate specificity of the cdk-activating kinase (CAK) is altered upon association with TFIIH. EMBO J. 16:1628–1637.
  • Schroeder, S. C., Schwer B., Shuman S., and Bentley D.. 2000. Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 14:2435–2440.
  • Serizawa, H., Conaway J. W., and Conaway R. C.. 1993. Phosphorylation of C-terminal domain of RNA polymerase II is not required in basal transcription. Nature 363:371–374.
  • Shah, K., Liu Y., Deirmengian C., and Shokat K. M.. 1997. Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates. Proc. Natl. Acad. Sci. USA 94:3565–3570.
  • Shah, K., and Shokat K. M.. 2002. A chemical genetic screen for direct v-Src substrates reveals ordered assembly of a retrograde signaling pathway. Chem. Biol. 9:35–47.
  • Sikorski, R. S., and Hieter P.. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19–27.
  • Tirode, F., Busso D., Coin F., and Egly J. M.. 1999. Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7. Mol. Cell 3:87–95.
  • Tora, L. 2002. A unified nomenclature for TATA box binding protein (TBP)-associated factors (TAFs) involved in RNA polymerase II transcription. Genes Dev. 16:673–675.
  • Valay, J.-G., Simon M., Dubois M.-F., Bensaude O., Facca C., and Faye G.. 1995. The KIN28 gene is required both for RNA polymerase II mediated transcription and phosphorylation of the Rpb1p CTD. J. Mol. Biol. 249:535–544.
  • Vincent, O., Kuchin S., Hong S. P., Townley R., Vyas V. K., and Carlson M.. 2001. Interaction of the Srb10 kinase with Sip4, a transcriptional activator of gluconeogenic genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 21:5790–5796.
  • Witucki, L. A., Huang X., Shah K., Liu Y., Kyin S., Eck M. J., and Shokat K. M.. 2002. Mutant tyrosine kinases with unnatural nucleotide specificity retain the structure and phospho-acceptor specificity of the wild-type enzyme. Chem. Biol. 9:25–33.
  • Yankulov, K. Y., and Bentley D. L.. 1997. Regulation of CDK7 substrate specificity by MAT1 and TFIIH. EMBO J. 16:1638–1646.
  • Yudkovsky, N., Ranish J. A., and Hahn S.. 2000. A transcription reinitiation intermediate that is stabilized by activator. Nature 408:225–229.

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