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Transcriptional Regulation

RPAP1, a Novel Human RNA Polymerase II-Associated Protein Affinity Purified with Recombinant Wild-Type and Mutated Polymerase Subunits

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Pages 7043-7058 | Received 24 Dec 2003, Accepted 14 May 2004, Published online: 27 Mar 2023

REFERENCES

  • Acker, J., Wintzerith M., Vigneron M., and Kedinger C.. 1992. Primary structure of the second largest subunit of human RNA polymerase II (or B). J. Mol. Biol. 226:1295–1299.
  • Armache, K. J., Kettenberger H., and Cramer P.. 2003. Architecture of initiation-competent 12-subunit RNA polymerase II. Proc. Natl. Acad. Sci. USA 100:6964–6968.
  • Awrey, D. E., Weilbaecher R. G., Hemming S. A., Orlicky S. M., Kane C. M., and Edwards A. M.. 1997. Transcription elongation through DNA arrest sites. A multistep process involving both RNA polymerase II subunit RPB9 and TFIIS. J. Biol. Chem. 272:14747–14754.
  • Bagby, S., Kim S., Maldonado E., Tong K. I., Reinberg D., and Ikura M.. 1995. Solution structure of the C-terminal core domain of human TFIIB: similarity to cyclin A and interaction with TATA-binding protein. Cell 82:857–867.
  • Bryant, G. O., and Ptashne M.. 2003. Independent recruitment in vivo by Gal4 of two complexes required for transcription. Mol. Cell 11:1301–1309.
  • Burton, Z. F., Ortolan L. G., and Greenblatt J.. 1986. Proteins that bind to RNA polymerase II are required for accurate initiation of transcription at the adenovirus 2 major late promoter. EMBO J. 5:2923–2930.
  • Bushnell, D. A., and Kornberg R. D.. 2003. Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription. Proc. Natl. Acad. Sci. USA 100:6969–6973.
  • Campbell, E. A., Muzzin O., Chlenov M., Sun J. L., Olson C. A., Weinman O., Trester-Zedlitz M. L., and Darst S. A.. 2002. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol. Cell 9:527–539.
  • Chambers, R. S., Wang B. Q., Burton Z. F., and Dahmus M. E.. 1995. The activity of COOH-terminal domain phosphatase is regulated by a docking site on RNA polymerase II and by the general transcription factors IIF and IIB. J. Biol. Chem. 270:14962–14969.
  • 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.
  • Choder, M., and Young R. A.. 1993. A portion of RNA polymerase II molecules has a component essential for stress responses and stress survival. Mol. Cell. Biol. 13:6984–6991.
  • Coates, J. C. 2003. Armadillo repeat proteins: beyond the animal kingdom. Trends Cell Biol. 13:463–471.
  • Conaway, J. W., and Conaway R. C.. 1989. A multisubunit transcription factor essential for accurate initiation by RNA polymerase II. J. Biol. Chem. 264:2357–2362.
  • Conaway, J. W., Shilatifard A., Dvir A., and Conaway R. C.. 2000. Control of elongation by RNA polymerase II. Trends Biochem. Sci. 25:375–380.
  • Conaway, R. C., Garrett K. P., Hanley J. P., and Conaway J. W.. 1991. Mechanism of promoter selection by RNA polymerase II: mammalian transcription factors alpha and beta gamma promote entry of polymerase into the preinitiation complex. Proc. Natl. Acad. Sci. USA 88:6205–6209.
  • Coulombe, B., and Burton Z. F.. 1999. DNA bending and wrapping around RNA polymerase: a “revolutionary” model describing transcriptional mechanisms. Microbiol. Mol. Biol. Rev. 63:457–478.
  • Cramer, P., Bushnell D. A., Fu J., Gnatt A. L., Maier-Davis B., Thompson N. E., Burgess R. R., Edwards A. M., David P. R., and Kornberg R. D.. 2000. Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288:640–649.
  • Cramer, P., Bushnell D. A., and Kornberg R. D.. 2001. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292:1863–1876.
  • Dey, A., Chitsaz F., Abbasi A., Misteli T., and Ozato K.. 2003. The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis. Proc. Natl. Acad. Sci. USA 100:8758–8763.
  • Douziech, M., Coin F., Chipoulet J. M., Arai Y., Ohkuma Y., Egly J. M., and Coulombe B.. 2000. Mechanism of promoter melting by the xeroderma pigmentosum complementation group B helicase of transcription factor IIH revealed by protein-DNA photo-cross-linking. Mol. Cell. Biol. 20:8168–8177.
  • Feaver, W. J., Gileadi O., Li Y., and Kornberg R. D.. 1991. CTD kinase associated with yeast RNA polymerase II initiation factor b. Cell 67:1223–1230.
  • Finkelstein, A., Kostrub C. F., Li J., Chavez D. P., Wang B. Q., Fang S. M., Greenblatt J., and Burton Z. F.. 1992. A cDNA encoding RAP74, a general initiation factor for transcription by RNA polymerase II. Nature 355:464–467.
  • Flores, O., Ha I., and Reinberg D.. 1990. Factors involved in specific transcription by mammalian RNA polymerase II. Purification and subunit composition of transcription factor IIF. J. Biol. Chem. 265:5629–5634.
  • Forget, D., Langelier M. F., Therien C., Trinh V., and Coulombe B.. 2004. Photo-cross-linking of a purified preinitiation complex reveals central roles for the RNA polymerase II mobile clamp and TFIIE in initiation mechanisms. Mol. Cell. Biol. 24:1122–1131.
  • Forget, D., Robert F., Grondin G., Burton Z. F., Greenblatt J., and Coulombe B.. 1997. RAP74 induces promoter contacts by RNA polymerase II upstream and downstream of a DNA bend centered on the TATA box. Proc. Natl. Acad. Sci. USA 94:7150–7155.
  • Fu, J., Gnatt A. L., Bushnell D. A., Jensen G. J., Thompson N. E., Burgess R. R., David P. R., and Kornberg R. D.. 1999. Yeast RNA polymerase II at 5 A resolution. Cell 98:799–810.
  • Gerard, M., Fischer L., Moncollin V., Chipoulet J. M., Chambon P., and Egly J. M.. 1991. Purification and interaction properties of the human RNA polymerase B(II) general transcription factor BTF2. J. Biol. Chem. 266:20940–20945.
  • Giaever, G., Chu A. M., Ni L., Connelly C., Riles L., Veronneau S., Dow S., Lucau-Danila A., Anderson K., Andre B., Arkin A. P., Astromoff A., El Bakkoury M., Bangham R., Benito R., Brachat S., Campanaro S., Curtiss M., Davis K., Deutschbauer A., Entian K. D., Flaherty P., Foury F., Garfinkel D. J., Gerstein M., Gotte D., Guldener U., Hegemann J. H., Hempel S., Herman Z., Jaramillo D. F., Kelly D. E., Kelly S. L., Kotter P., LaBonte D., Lamb D. C., Lan N., Liang H., Liao H., Liu L., Luo C., Lussier M., Mao R., Menard P., Ooi S. L., Revuelta J. L., Roberts C. J., Rose M., Ross-Macdonald P., Scherens B., Schimmack G., Shafer B., Shoemaker D. D., Sookhai-Mahadeo S., Storms R. K., Strathern J. N., Valle G., Voet M., Volckaert G., Wang C. Y., Ward T. R., Wilhelmy J., Winzeler E. A., Yang Y., Yen G., Youngman E., Yu K., Bussey H., Boeke J. D., Snyder M., Philippsen P., Davis R. W., and Johnston M.. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387–391.
  • Gnatt, A., Fu J., and Kornberg R. D.. 1997. Formation and crystallization of yeast RNA polymerase II elongation complexes. J. Biol. Chem. 272:30799–30805.
  • Gnatt, A. L., Cramer P., Fu J., Bushnell D. A., and Kornberg R. D.. 2001. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science 292:1876–1882.
  • Ha, I., Lane W. S., and Reinberg D.. 1991. Cloning of a human gene encoding the general transcription initiation factor IIB. Nature 352:689–695.
  • Hampsey, M. 1998. Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. Mol. Biol. Rev. 62:465–503.
  • Hazbun, T. R., Malmstrom L., Anderson S., Graczyk B. J., Fox B., Riffle M., Sundin B. A., Aranda J. D., McDonald W. H., Chiu C. H., Snydsman B. E., Bradley P., Muller E. G., Fields S., Baker D., Yates III J. R., and Davis T. N.. 2003. Assigning function to yeast proteins by integration of technologies. Mol. Cell 12:1353–1365.
  • Hegde, P., Qi R., Abernathy K., Gay C., Dharap S., Gaspard R., Hughes J. E., Snesrud E., Lee N., and Quackenbush J.. 2000. A concise guide to cDNA microarray analysis. BioTechniques 29:548–556.
  • Ho, C. K., and Shuman S.. 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.
  • Hodo, H. G., III, and Blatti S. P.. 1977. Purification using polyethylenimine precipitation and low molecular weight subunit analyses of calf thymus and wheat germ DNA-dependent RNA polymerase II. Biochemistry 16:2334–2343.
  • Holstege, F. C., Fiedler U., and Timmers H. T.. 1997. Three transitions in the RNA polymerase II transcription complex during initiation. EMBO J. 16:7468–7480.
  • Holstege, F. C., Tantin D., Carey M., van der Vliet P. C., and Timmers H. T.. 1995. The requirement for the basal transcription factor IIE is determined by the helical stability of promoter DNA. EMBO J. 14:810–819.
  • Holstege, F. C., van der Vliet P. C., and Timmers H. T.. 1996. Opening of an RNA polymerase II promoter occurs in two distinct steps and requires the basal transcription factors IIE and IIH. EMBO J. 15:1666–1677.
  • Huber, A. H., Nelson W. J., and Weis W. I.. 1997. Three-dimensional structure of the armadillo repeat region of beta-catenin. Cell 90:871–882.
  • Huh, W. K., Falvo J. V., Gerke L. C., Carroll A. S., Howson R. W., Weissman J. S., and O'Shea E. K.. 2003. Global analysis of protein localization in budding yeast. Nature 425:686–691.
  • Ingles, C. J., Shales M., Cress W. D., Triezenberg S. J., and Greenblatt J.. 1991. Reduced binding of TFIID to transcriptionally compromised mutants of VP16. Nature 351:588–590.
  • Ito, T., Chiba T., Ozawa R., Yoshida M., Hattori M., and Sakaki Y.. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98:4569–4574.
  • Jiang, Y., Triezenberg S. J., and Gralla J. D.. 1994. Defective transcriptional activation by diverse VP16 mutants associated with a common inability to form open promoter complexes. J. Biol. Chem. 269:5505–5508.
  • Kim, J. L., Nikolov D. B., and Burley S. K.. 1993. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365:520–527.
  • Kim, Y., Geiger J. H., Hahn S., and Sigler P. B.. 1993. Crystal structure of a yeast TBP/TATA-box complex. Nature 365:512–520.
  • Kimura, M., Suzuki H., and Ishihama A.. 2002. Formation of a carboxy-terminal domain phosphatase (Fcp1)/TFIIF/RNA polymerase II (Pol II) complex in Schizosaccharomyces pombe involves direct interaction between Fcp1 and the Rpb4 subunit of Pol II. Mol. Cell. Biol. 22:1577–1588.
  • Kobor, M. S., Archambault J., Lester W., Holstege F. C., Gileadi O., Jansma D. B., Jennings E. G., Kouyoumdjian F., Davidson A. R., Young R. A., and Greenblatt J.. 1999. An unusual eukaryotic protein phosphatase required for transcription by RNA polymerase II and CTD dephosphorylation in S. cerevisiae. Mol. Cell 4:55–62.
  • Kobor, M. S., Simon L. D., Omichinski J., Zhong G., Archambault J., and Greenblatt J.. 2000. A motif shared by TFIIF and TFIIB mediates their interaction with the RNA polymerase II carboxy-terminal domain phosphatase Fcp1p in Saccharomyces cerevisiae. Mol. Cell. Biol. 20:7438–7449.
  • Krogan, N. J., Kim M., Ahn S. H., Zhong G., Kobor M. S., Cagney G., Emili A., Shilatifard A., Buratowski S., and Greenblatt J. F.. 2002. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol. Cell. Biol. 22:6979–6992.
  • Lagrange, T., Kapanidis A. N., Tang H., Reinberg D., and Ebright R. H.. 1998. New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes Dev. 12:34–44.
  • Langelier, M. F., Forget D., Rojas A., Porlier Y., Burton Z. F., and Coulombe B.. 2001. Structural and functional interactions of transcription factor (TF) IIA with TFIIE and TFIIF in transcription initiation by RNA polymerase II. J. Biol. Chem. 276:38652–38657.
  • Lu, H., Zawel L., Fisher L., Egly J. M., and Reinberg D.. 1992. Human general transcription factor IIH phosphorylates the C-terminal domain of RNA polymerase II. Nature 358:641–645.
  • Maldonado, E., Ha I., Cortes P., Weis L., and Reinberg D.. 1990. Factors involved in specific transcription by mammalian RNA polymerase II: role of transcription factors IIA, IID, and IIB during formation of a transcription-competent complex. Mol. Cell. Biol. 10:6335–6347.
  • Marton, M. J., DeRisi J. L., Bennett H. A., Iyer V. R., Meyer M. R., Roberts C. J., Stoughton R., Burchard J., Slade D., Dai H., Bassett D. E., Jr., Hartwell L. H., Brown P. O., and Friend S. H.. 1998. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat. Med. 4:1293–1301.
  • Mizuguchi, K., Deane C. M., Blundell T. L., and Overington J. P.. 1998. HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci. 7:2469–2471.
  • Murakami, K. S., Masuda S., Campbell E. A., Muzzin O., and Darst S. A.. 2002. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 296:1285–1290.
  • Murakami, K. S., Masuda S., and Darst S. A.. 2002. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution. Science 296:1280–1284.
  • Nikolov, D. B., Chen H., Halay E. D., Usheva A. A., Hisatake K., Lee D. K., Roeder R. G., and Burley S. K.. 1995. Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature 377:119–128.
  • Nissen, R. M., and Yamamoto K. R.. 2000. The glucocorticoid receptor inhibits NFkappaB by interfering with serine-2 phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev. 14:2314–2329.
  • No, D., Yao T. P., and Evans R. M.. 1996. Ecdysone-inducible gene expression in mammalian cells and transgenic mice. Proc. Natl. Acad. Sci. USA 93:3346–3351.
  • Ohkuma, Y., Hashimoto S., Wang C. K., Horikoshi M., and Roeder R. G.. 1995. Analysis of the role of TFIIE in basal transcription and TFIIH-mediated carboxy-terminal domain phosphorylation through structure-function studies of TFIIE-alpha. Mol. Cell. Biol. 15:4856–4866.
  • 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.
  • Ohkuma, Y., Sumimoto H., Hoffmann A., Shimasaki S., Horikoshi M., and Roeder R. G.. 1991. Structural motifs and potential sigma homologies in the large subunit of human general transcription factor TFIIE. Nature 354:398–401.
  • Orphanides, G., Lagrange T., and Reinberg D.. 1996. The general transcription factors of RNA polymerase II. Genes Dev. 10:2657–2683.
  • Pan, G., and Greenblatt J.. 1994. Initiation of transcription by RNA polymerase II is limited by melting of the promoter DNA in the region immediately upstream of the initiation site. J. Biol. Chem. 269:30101–30104.
  • Peterson, M. G., Inostroza J., Maxon M. E., Flores O., Admon A., Reinberg D., and Tjian R.. 1991. Structure and functional properties of human general transcription factor IIE. Nature 354:369–373.
  • Pokholok, D. K., Hannett N. M., and Young R. A.. 2002. Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol. Cell 9:799–809.
  • Puig, O., Caspary F., Rigaut G., Rutz B., Bouveret E., Bragado-Nilsson E., Wilm M., and Seraphin B.. 2001. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24:218–229.
  • Rachez, C., and Freedman L. P.. 2001. Mediator complexes and transcription. Curr. Opin. Cell Biol. 13:274–280.
  • 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.
  • Robert, F., Douziech M., Forget D., Egly J. M., Greenblatt J., Burton Z. F., and Coulombe B.. 1998. Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF. Mol. Cell 2:341–351.
  • Rodriguez, C. R., Cho E. J., Keogh M. C., Moore C. L., Greenleaf A. L., and Buratowski S.. 2000. Kin28, the TFIIH-associated carboxy-terminal domain kinase, facilitates the recruitment of mRNA processing machinery to RNA polymerase II. Mol. Cell. Biol. 20:104–112.
  • Schaffer, A. A., Wolf Y. I., Ponting C. P., Koonin E. V., Aravind L., and Altschul S. F.. 1999. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics 15:1000–1011.
  • Serizawa, H., Conaway R. C., and Conaway J. W.. 1992. A carboxyl-terminal-domain kinase associated with RNA polymerase II transcription factor delta from rat liver. Proc. Natl. Acad. Sci. USA 89:7476–7480.
  • Serizawa, H., Makela T. P., Conaway J. W., Conaway R. C., Weinberg R. A., and Young R. A.. 1995. Association of Cdk-activating kinase subunits with transcription factor TFIIH. Nature 374:280–282.
  • Shiekhattar, R., Mermelstein F., Fisher R. P., Drapkin R., Dynlacht B., Wessling H. C., Morgan D. O., and Reinberg D.. 1995. Cdk-activating kinase complex is a component of human transcription factor TFIIH. Nature 374:283–287.
  • Skaar, D. A., and Greenleaf A. L.. 2002. The RNA polymerase II CTD kinase CTDK-I affects pre-mRNA 3′ cleavage/polyadenylation through the processing component Pti1p. Mol. Cell 10:1429–1439.
  • Sluder, A. E., Price D. H., and Greenleaf A. L.. 1988. Elongation by Drosophila RNA polymerase II. Transcription of 3′-extended DNA templates. J. Biol. Chem. 263:9917–9925.
  • Sopta, M., Carthew R. W., and Greenblatt J.. 1985. Isolation of three proteins that bind to mammalian RNA polymerase II. J. Biol. Chem. 260:10353–10360.
  • Sumimoto, H., Ohkuma Y., Sinn E., Kato H., Shimasaki S., Horikoshi M., and Roeder R. G.. 1991. Conserved sequence motifs in the small subunit of human general transcription factor TFIIE. Nature 354:401–404.
  • Takahashi, Y., Rayman J. B., and Dynlacht B. D.. 2000. Analysis of promoter binding by the E2F and pRB families in vivo: distinct E2F proteins mediate activation and repression. Genes Dev. 14:804–816.
  • 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.
  • Vassylyev, D. G., Sekine S., Laptenko O., Lee J., Vassylyeva M. N., Borukhov S., and Yokoyama S.. 2002. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature 417:712–719.
  • Westover, K. D., Bushnell D. A., and Kornberg R. D.. 2004. Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science 303:1014–1016.
  • Wu, L. F., Hughes T. R., Davierwala A. P., Robinson M. D., Stoughton R., and Altschul S. J.. 2002. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat. Genet. 31:255–265.
  • Yang, Y. H., and Speed T.. 2002. Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3:579–588.
  • Young, R. A. 1991. RNA polymerase II. Annu. Rev. Biochem. 60:689–715.
  • Zhang, G., Campbell E. A., Minakhin L., Richter C., Severinov K., and Darst S. A.. 1999. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell 98:811–824.

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