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Transcriptional Regulation

Mechanism of Promoter Melting by the Xeroderma Pigmentosum Complementation Group B Helicase of Transcription Factor IIH Revealed by Protein-DNA Photo-Cross-Linking

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Pages 8168-8177 | Received 23 Jun 2000, Accepted 26 Jul 2000, Published online: 28 Mar 2023

REFERENCES

  • Bagby, S., Kim, S. J., 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
  • Coin, F., Bergmann, E., Tremeau-Bravard, A., and Egly, J. M.. 1999. Mutations in XPB and XPD helicases found in xeroderma pigmentosum patients impair the transcription function of TFIIH. EMBO J. 18:1357–1366
  • 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, 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
  • Coulombe, B., Li, J., and Greenblatt, J.. 1994. Topological localization of the human transcription factors IIA, IIB, TATA box-binding protein, and RNA polymerase II-associated protein 30 on a class II promoter. J. Biol. Chem. 269:19962–19967
  • 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
  • Dahmus, M. E.. 1996. Reversible phosphorylation of the C-terminal domain of RNA polymerase II. J. Biol. Chem. 271:19009–19012
  • Darst, S. A., Edwards, A. M., Kubalek, E. W., and Kornberg, R. D.. 1991. Three-dimensional structure of yeast RNA polymerase II at 16 A resolution. Cell 66:121–128
  • Douziech, M., Forget, D., Greenblatt, J., and Coulombe, B.. 1999. Topological localization of the carboxyl-terminal domain of RNA polymerase II in the initiation complex. J. Biol. Chem. 274:19868–19873
  • Drapkin, R., Reardon, J. T., Ansari, A., Huang, J. C., Zawel, L., Ahn, K., Sancar, A., and Reinberg, D.. 1994. Dual role of TFIIH in DNA excision repair and in transcription by RNA polymerase II. Nature 368:769–772
  • Evans, E., Moggs, J. G., Hwang, J. R., Egly, J. M., and Wood, R. D.. 1997. Mechanism of open complex and dual incision formation by human excision repair factors. EMBO J. 16:6559–6573
  • 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
  • Fisher, R. P., and Morgan, D. O.. 1994. A novel cyclin associates with MO15/CDK7 to form the CDK-activating kinase. Cell 78:713–724
  • 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
  • Flores, O., Lu, H., Killeen, M., Greenblatt, J., Burton, Z. F., and Reinberg, D.. 1991. The small subunit of transcription factor IIF recruits RNA polymerase II into the pre-initiation complex. Proc. Natl. Acad. Sci. USA 88:9999–10003
  • Forget, D., Robert, F., Grondin, G., Burton, Z. F., Greenblatt, J., and Coulombe, B.. 1997. RAP74 induces promoter contact by RNA polymerase II upstream and downstream of a DNA bend centered on the TATA box. Proc. Natl. Acad. Sci. USA 94:7150–7155
  • 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
  • Goodrich, J. A., and Tjian, R.. 1994. Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II. Cell 77:145–156
  • Groft, C. M., Uljon, S. N., Wang, R., and Werner, M. H.. 1998. Structural homology between the RAP30 DNA-binding domain and linker histone H5: implications for preinitiation complex assembly. Proc. Natl. Acad. Sci. USA 95:9117–9122
  • Hampsey, M.. 1998. Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. Mol. Biol. Rev. 62:465–503
  • 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
  • Inostroza, J., Flores, O., and Reinberg, D.. 1991. Factors involved in specific transcription by mammalian RNA polymerase II. Purification and functional analysis of general transcription factor IIE. J. Biol. Chem. 266:9304–9308
  • 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, T. K., Lagrange, T., Wang, Y. H., Griffith, J. D., Reinberg, D., and Ebright, R. H.. 1997. Trajectory of DNA in the RNA polymerase II transcription preinitiation complex. Proc. Natl. Acad. Sci. USA 94:12268–12273
  • Kim, T. K., Ebright, R. H., and Reinberg, D.. 2000. Mechanism of ATP-dependent promoter melting by transcription factor TFIIH. Science 288:1418–1421
  • 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
  • Lagrange, T., Kim, T. K., Orphanides, G., Ebright, Y. W., Ebright, R. H., and Reinberg, D.. 1996. High-resolution mapping of nucleoprotein complexes by site-specific protein-DNA photocrosslinking: organization of the human TBP-TFIIA-TFIIB-DNA quaternary complex. Proc. Natl. Acad. Sci. USA 93:10620–10625
  • Lei, L., Ren, D., and Burton, Z. F.. 1999. The RAP74 subunit of transcription factor IIF has a similar role in isomerization of the initiation and the elongation complexes. Mol. Cell. Biol. 19:8372–8382
  • Lei, L., Ren, D., Finkelstein, A., and Burton, Z. F.. 1998. Functions of the N- and C-terminal domains of human RAP74 in transcriptional initiation, elongation, and recycling of RNA polymerase II. Mol. Cell. Biol. 18:2130–2142
  • Lohman, T. M., and Bjornson, K. P.. 1996. Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65:169–214
  • 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
  • Moreland, R. J., Tirode, F., Yan, Q., Conaway, J. W., Egly, J. M., and Conaway, R. C.. 1999. A role for the TFIIH XPB DNA helicase in promoter escape by RNA polymerase II. J. Biol. Chem. 274:22127–22130
  • 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
  • Oelgeschlager, T., Chiang, C. M., and Roeder, R. G.. 1996. Topology and reorganization of a human TFIID-promoter complex. Nature 382:735–738
  • 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 TFIIEα. 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., Horikoshi, M., and Roeder, R. G.. 1990. Factors involved in specific transcription by mammalian RNA polymerase II: purification and characterization of general transcription factor TFIIE. Proc. Natl. Acad. Sci. USA 87:9163–9167
  • Okamoto, T., Yamamoto, S., Watanabe, Y., Ohta, T., Hanaoka, F., Roeder, R. G., and Ohkuma, Y.. 1998. Analysis of the role of TFIIE in transcriptional regulation through structure-function studies of the TFIIEβ subunit. J. Biol. Chem. 273:19866–19876
  • Okuda, M., Watanabe, Y., Okamura, H., Hanaoka, F., Ohkuma, Y., and Nishimura, Y.. 2000. Structure of the central core domain of TFIIEβ with a novel double-stranded DNA-binding surface. EMBO J. 19:1346–1356
  • Orphanides, G., Lagrange, T., and Reinberg, D.. 1996. The general initiation factors of RNA polymerase II. Genes Dev. 10:2657–2683
  • Pan, G. H., 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
  • Parvin, J. D., and Sharp, P. A.. 1993. DNA topology and a minimal set of basal factors for transcription by RNA polymerase II. Cell 73:533–540
  • Poglitsch, C. L., Meredith, G. D., Gnatt, A. L., Jensen, G. J., Chang, W.-H., Fu, J., and Kornberg, R. D.. 1999. Electron crystal structure of an RNA polymerase II transcription elongation complex. Cell 98:791–798
  • Rivetti, C., Guthold, M., and Bustamante, C.. 1999. Wrapping of DNA around the E. coli RNA polymerase open promoter complex. EMBO J. 18:4464–4475
  • Robert, F., and Coulombe B.. The use of site-specific protein-DNA photo-crosslinking to analyze the molecular organization of the RNA polymerase II initiation complex. Methods Mol. Biol., in press.
  • Robert, F., Forget, D., Li, J., Greenblatt, J., and Coulombe, B.. 1996. Localization of subunits of transcription factors IIE and IIF immediately upstream of the transcriptional initiation site of the adenovirus major late promoter. J. Biol. Chem. 271:8517–8520
  • 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
  • Roy, R., Adamczewski, J. P., Seroz, T., Vermeulen, W., Tassan, J. P., Schaeffer, L., Nigg, E. A., Hoeijmakers, J. H. J., and Egly, J. M.. 1994. The MO15 cell cycle kinase is associated with the TFIIH transcription-DNA repair factor. Cell 79:1093–1101
  • Schaeffer, L., Moncollin, V., Roy, R., Staub, A., Mezzina, M., Sarasin, A., Weeda, G., Hoeijmakers, J. H. J., and Egly, J. M.. 1994. The ERCC2/DNA repair protein is associated with the class II BTF2/TFIIH transcription repair factor. EMBO J. 13:2388–2392
  • Schaeffer, L., Roy, R., Humbert, S., Moncollin, V., Vermeulen, W., Hoeijmakers, J. H. J., Chambon, P., and Egly, J. M.. 1993. DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor. Science 260:58–63
  • Schultz, P., Fribourg, S., Poterszman, A., Mallouh, V., Moras, D., and Egly, J. M.. 2000. Molecular structure of human TFIIH. Cell 102:599–607
  • 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., Conaway, R. C., and Conaway, J. W.. 1993. Multifunctional RNA polymerase II initiation factor delta from rat liver. Relationship between carboxyl-terminal domain kinase, ATPase, and helicase activities. J. Biol. Chem. 268:17300–17308
  • 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
  • Svejstrup, J. Q., Vichi, P., and Egly, J. M.. 1996. The multiple roles of transcription/repair factor TFIIH. Trends Biochem. Sci. 21:346–350
  • Tantin, D., and Carey, M.. 1994. A heteroduplex template circumvents the energetic requirement for ATP during activated transcription by RNA polymerase II. J. Biol. Chem. 269:17397–17400
  • Timmers, H. T. M.. 1994. Transcription initiation by RNA polymerase II does not require hydrolysis of the β-γ phosphoanhydride bond of ATP. EMBO J. 13:391–399
  • 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
  • Tyree, C. M., George, C. P., Lira-Devito, L. M., Wampler, S. L., Dahmus, M. E., Zawel, L., and Kadonaga, J. T.. 1993. Identification of a minimal set of proteins that is sufficient for accurate initiation of transcription by RNA polymerase II. Genes Dev. 7:1254–1265
  • Velankar, S. S., Soultanas, P., Dillingham, M. S., Subramanya, H. S., and Wigley, D. B.. 1999. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97:75–84
  • Wang, B. Q., and Burton, Z. F.. 1995. Functional domains of human RAP74 including a masked polymerase binding domain. J. Biol. Chem. 270:27035–27044
  • Wang, Z. G., Buratowski, S., Svejstrup, J. Q., Feaver, W. J., Wu, X. H., Kornberg, R. D., Donahue, T. F., and Friedberg, E. C.. 1995. The yeast TFB1 and SSL1 genes, which encode subunits of transcription factor IIH, are required for nucleotide excision repair and RNA polymerase II transcription. Mol. Cell. Biol. 15:2288–2293
  • Weeda, G., van Ham, R. C. A., Vermeulen, W., Bootsma, D., van der Eb, A. J., and Hoeijmakers, J. H. J.. 1990. A presumed DNA helicase encoded by ERCC-3 is involved in the human repair disorders xeroderma pigmentosum and Cockayne's syndrome. Cell 62:777–791
  • Yan, M., and Gralla, J. D.. 1997. Multiple ATP-dependent steps in RNA polymerase II promoter melting and initiation. EMBO J. 16:7457–7467
  • Yokomori, K., Verrijzer, C. P., and Tijan, R.. 1998. An interplay between TATA box-binding protein and transcription factors IIE and IIA modulates DNA binding and transcription. Proc. Natl. Acad. Sci. USA 95:6722–6727
  • 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 a 3.3 A resolution. Cell 98:811–824

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