Multiple functions of general transcription factors TFIIE and TFIIH in transcription: Possible points of regulation by trans-acting factors

Journal of Biochemistry

Volumn 122, Issue 3, 1997, Pages 481-489

  Ohkuma, Yoshiaki ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

General transcription factors; Promoter clearance; RNA polymerase II; TFIIE; TFIIH

Indexed keywords

RNA POLYMERASE II; TATA BINDING PROTEIN; TRANSCRIPTION FACTOR;

CELL CYCLE; COMPLEX FORMATION; DNA PROTEIN COMPLEX; ENZYME ACTIVITY; EXCISION REPAIR; HUMAN; PROMOTER REGION; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; REVIEW; TATA BOX; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

EID: 0030753149     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.jbchem.a021777     Document Type: Review

References (79)

1. von Hippel, P.H., Bear, D.G., Morgan, W.D., and McSwiggen, J.A. (1984) Protein-nucleic acid interactions in transcription: A molecular analysis. Annu. Rev. Biochem. 53, 389-446
2. McClure, W.R. (1985) Mechanism and control of transcription initiation in prokaryotes. Annu. Rev. Biochem. 54, 171-204
3. Roeder, R.G. (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci. 21, 327-335
4. Orphanides, G., Lagrange, T., and Reinberg, D. (1996) The general transcription factors of RNA polymerase II. Genes Dev. 10, 2657-2683
5. Nikolov, D.B. and Burley, S.K. (1997) RNA polymerase II transcription initiation: A structural view. Proc. Natl. Acad. Sci. USA 94, 15-22
6. Nikolov, D.B., Hu, S.-H., Lin, J., Gasch, A., Hoffmann, A., Horikoshi, M., Chua, N.-H., Roeder, R.G., and Burley, S.K. (1992) Crystal structure of TFIID TATA-box binding protein. Nature 360, 40-46
7. Burke, T.W. and Kadonaga, J.T. (1996) Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. Genes Dev. 10, 711-724
8. Martinez, E., Chiang, C.-M., Ge, H., and Roeder, R.G. (1994) TAFs in TFIID function through the initiator to direct basal transcription from a TATA-less class II promoter. EMBO J. 13, 3115-3126
9. Kaufmann, J., Verrijzer, C.P., Shao, J., and Smale, S.T. (1996) CIF, an essential cofactor for TFIID-dependent initiator function. Genes Dev. 10, 873-886
10. Koleske, A.J. and Young, R.A. (1995) The RNA polymerase II holoenzyme and its implications for gene regulation. Trends Biochem. Sci. 20, 113-116
11. Björklund, S. and Kim, Y.-J. (1996) Mediator of transcriptional regulation. Trends Biol. Sci. 21, 335-337
12. Chao, D.M., Gadbois, E.L., Murray, P.J., Anderson, S.F., Sonu, M.S., Parvin, J.D., and Young, R.A. (1996) A mammalian SRB protein associated with an RNA polymerase II holoenzyme. Nature 380, 82-85
13. Maldonado, E., Sheikhattar, R., Sheldon, M., Cho, H., Drapkin, R., Rickert, P., Lees, E., Anderson, C.W., Linn, S., and Reinberg, D. (1996) A human RNA polymerase II complex associtated with SRB and DNA-repair proteins. Nature 381, 86-89
14. Burley, S.K. and Roeder, R.G. (1996) Biochemistry and structural biology of transcription factor IID (TFIID). Annu. Rev. Biochem. 65, 769-799
15. Tang, H., Sun, X., Reinberg, D., and Ebright, R.H. (1996) Protein-protein interactions in eukaryotic transcription initiation: Structure of the preinitiation complex. Proc. Natl. Acad. Sci. USA 93, 1119-1124
16. 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 photo-crosslinking: Organization of the human TBP-TFIIA-TFIIB-DNA quaternary complex. Proc. Natl. Acad. Sci. USA 93, 10620-10625
17. Hoffmann, A., Sinn, E., Yamamoto, T., Wang, J., Roy, A., Horikoshi, M., and Roeder, R.G. (1990) Highly conserved core domain and unique N terminus with presumptive regulatory motifs in a human TATA factor (TFIID). Nature 346, 387-390
18. Hernandez, N. (1993) TBP, a universal eukaryotic transcription factor? Genes Dev. 7, 1291-1308
19. 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
20. 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
21. Tansey, W.P. and Herr, W. (1997) TAFs: Guilt by association? Cell 88, 729-732
22. Verrijzer, C.P. and Tjian, R. (1996) TAFs mediate transcriptional activation and promoter selectivity. Trends Biol. Sci. 21, 338-342
23. Oelgeschläger, T., Chiang, C.-M., and Roeder, R.G. (1996) Topology and reorganization of a human TFIID-promoter complex. Nature 382, 735-738
24. Hoffmann, A., Chiang, C.-M., Oelgeschläger, T., Xie, X., Burley, S.K., Nakatani, Y., and Roeder, R.G. (1996) A histone octamer-like structure within TFIID. Nature 380, 356-359
25. Hoffmann, A. and Roeder, R.G. (1996) Cloning and characterization of human TAF20/15. Multiple interactions suggest a central role in TFIID complex formation. J. Biol. Chem. 271, 18194-18202
26. 11250 subunit of TFIID has histone acetyltransferase activity. Cell 87, 1261-1270
27. 11250 is a bipartite protein kinase that phosphorylates the basal transcription factor RAP74. Cell 84, 781-790
28. 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
29. 11250: a TBP-associated factor implicated in cell-cycle regulation. Nature 362, 175-179
30. Hisatake, K., Hasegawa, S., Takada, R., Nakatani, Y., Horikoshi, M., and Roeder, R.G. (1993) The p250 subunit of native TATA box-binding factor TFIID is the cell-cycle regulatory protein CCG1. Nature 362, 179-181
31. 11250 gene is mutated in the thermosensitive G1 mutants of the BHK21 cell line derived from golden hamster. Gene 141, 267-270
32. 2/M but not for general transcription activation. Genes Dev. 10, 2368-2380
33. Usuda, Y., Kubota, A., Berk, A.J., and Handa, H. (1991) Affinity purification of transcription factor IIA from HeLa cell nuclear extracts. EMBO J. 10, 2305-2310
34. Ma, D., Watanabe, H., Mermelstein, F., Admon, A., Oguri, K., Sun, X., Wada, T., Imai, T., Shiroya, T., Reinberg, D., and Handa, H. (1993) Isolation of a cDNA encoding the largest subunit of TFIIA reveals functions important for activated transcription. Genes Dev. 7, 2246-2257
35. DeJong, J., Bernstein, R., and Roeder, R.G. (1995) Human general transcription factor TFIIA: Characterization of a cDNA encoding the small subunit and requirement for basal and activated transcription. Proc. Natl. Acad. Sci. USA 92, 3313-3317
36. Ma, D., Olave, I., Merino, A., and Reinberg, D. (1996) Separation of the transcriptional coactivator and antirepression functions of transcription factor IIA. Proc. Natl. Acad. Sci. USA 93, 6583-6588
37. 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
38. 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
39. Zhu, W., Zheng, Q., Colangelo, M., Lewis, M., Summers, M.F., and Scott, R.A. (1996) The N-terminal domain of TFIIB from Pyrococcus furiosis forms a zinc ribbon. Nature Struct. Biol. 3, 122-124
40. Pinto, I., Ware, D.E., and Hampsey, M. (1992) The yeast SUA7 gene encodes a homolog of human transcription factor TFIIB and is required for normal start site selection in vivo. Cell 68, 977-988
41. Leuther, K.K., Bushnell, D.A., and Kornberg, R.D. (1996) Two-dimensional crystallography of TFIIB- and IIE-RNA polymerase II complexes: Implications for start site selection and initiation complex formation. Cell 85, 773-779
42. Conaway, R.C. and Conaway, J.W. (1993) General initiation factors for RNA polymerase II. Annu. Rev. Biochem. 62, 161-190
43. Flores, O., Lu, H., Kileen, M., Greenblatt, J., Burton, Z.F., and Reinberg, D. (1991) The small subunit of transcription factor IIF recruits RNA polymerase II into the preinitiation complex. Proc. Natl. Acad. Sci. USA 88, 9999-10003
44. Kileen, M.T. and Greenblatt, J.F. (1992) The general transcription factor RAP30 binds to RNA polymerase II and prevents it from binding nonspecifically to DNA. Mol. Cell. Biol. 12, 30-37
45. 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
46. Sun, Z.-W. and Hampsey, M. (1995) Identification of the gene (SSU71/TFG1) encoding the largest subunit of transcription factor TFIIF as a suppressor of a TFIIB mutation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 92, 3127-3131
47. Usheva, A., Maldonado, E., Goldring, A., Lu, H., Houbavi, D., Reinberg, D., and Aloni, Y. (1992) Specific interaction between the nonphosphorylated form of RNA polymerase II and the TATA-binding protein. Cell 69, 871-881
48. Zawel, L., Kumar, K.P., and Reinberg, D. (1995) Recycling of the general transcription factors during RNA polymerase II transcription. Genes Dev. 9, 1479-1490
49. Reines, D., Conaway, J.W., and Conaway, R.C. (1996) The RNA polymerase II general elongation factors. Trends Biochem. Sci. 21, 351-355
50. 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
51. Ohkuma, Y., Sumimoto, H., Hoffmann, A., Shimasaki, S., Horikoshi, M., and Roeder, R.G. (1991) Structural motifs and potential σ homologies in the large subunit of human general transcription factor TFIIE. Nature 354, 398-402
52. Peterson, M.G., Inostroza, J., Maxon, M.E., Flores, O., Admon, A., Reinberg, D., and Tjian, R. (1991) Structure and function of the recombinant subunits of human TFIIE. Nature 354, 369-373
53. 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-α. Mol. Cell. Biol. 15, 4856-4866
54. 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
55. Svejstrup, J.Q., Vichi, P., and Egly, J.-M. (1996) The multiple roles of transcription/repair factor TFIIH. Trends Biochem. Sci. 21, 346-350
56. Drapkin, R., Reardon, J.T., Ansali, 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
57. 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
58. Yankulov, K.Y. and Bentley, D.L. (1997) Regulation of CDK7 substrate specificity by MAT1 and TFIIH. EMBO J. 16, 1638-1646
59. Holstege, F.C.P., van der Vliet, P.C., and Timmers, H.T.M. (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
60. Holstege, F.C.P., Tantin, D., Carey, M., van der Vliet, P.C., and Timmers, H.T.M. (1995) The requirement for the basal transcription factor IIE is determined by the helical stability of promoter DNA. EMBO J. 14, 810-819
61. Parvin, J.D. and Sharp, P.A. (1993) DNA topology and a minimal set of basal factors initiate transcription by RNA polymerase II. Cell 73, 533-540
62. 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
63. Dvir, A., Conaway, R.C., and Conaway, J.W. (1996) Promoter escape by RNA polymerase II. A role for ATP cofactor in suppression of arrest by polymerase at promoter-proximal sites. J. Biol. Chem. 271, 23352-23356
64. Weeks, J.R., Hardin, S.E., Shen, J., Lee, J.M., and Greenleaf, A.L. (1993) Locus-specific variation in phosphorylation state of RNA polymerase II in vivo: Correlation with gene activity and transcript processing. Genes Dev. 7, 2329-2344
65. O'Brien, T., Hardin, S., Greenleaf, A., and Lis, J. (1994) Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation. Nature 370, 75-77
66. Friedberg, E.C. (1996) Relationships between DNA repair and transcription. Annu. Rev. Biochem. 65, 15-42
67. Park, C.-H., Mu, D., Reardon, J.T., and Sancar, A. (1995) The general transcription-repair factor TFIIH is recruited to the excision repair complex by the XPA protein independent of the TFIIE transcription factor. J. Biol. Chem. 270, 4896-4902
68. Selby, C.P. and Sancar, A. (1997) Human transcription-repair coupling factor CSB/ERCC6 is a DNA-stimulated ATPase but is not a helicase and does not disrupt the ternary transcription complex of stalled RNA polymerase II. J. Biol. Chem. 272, 1885-1890
69. Xiao, H., Pearson, A., Coulombe, B., Truant, R., Zhang, S., Regier, J.L., Triezenberg, S.J., Reinberg, D., Flores, O., Ingles, C.J., and Greenblatt, J. (1994) Binding of basal transcription factor TFIIH to the acidic activation domains of VP16 and p53. Mol. Cell. Biol. 14, 7013-7024
70. Parada, C. and Roeder, R.G. (1996) Enhanced processivity of RNA polymerase II triggered by Tat-induced phosphorylation of its carboxy-terminal domain. Nature 384, 375-378
71. Tong, X., Drapkin, R., Reinberg, D., and Kieff, E. (1995) The 62- and 80-kDa subunits of transcription factor IIH mediate the interaction with Epstein-Barr virus nuclear protein 2. Proc. Natl. Acad. Sci. USA 92, 3259-3263
72. Qadri, I., Conaway, J.W., Conaway, R.C., Schaack, J., and Siddiqui, A. (1996) Hepatitis B virus transactivator protein, HBx, associates with the components of TFIIH and stimulates the DNA helicase activity of TFIIH. Proc. Natl. Acad. Sci. USA 93, 10578-10583
73. Henning, K.A., Li, L., Iyer, N., McDaniel, L.D., Reagan, M.S., Legerski, R., Schultz, R.A., Stefanini, M., Lehman, A.R., Mayne, L.V., and Friedberg, E.C. (1995) The Cockayne syndrome group A gene encodes a WD repeat protein that interacts with CSB protein and a subunit of RNA polymerase II TFIIH. Cell 82, 555-564
74. Tong, X., Drapkin, R., Yalamanchili, R., Mosialos, G., and Kieff, E. (1995) The Epstein-Barr virus nuclear protein 2 acidic domain forms a complex with a novel cellular coactivator that can interact with TFIIE. Mol. Cell. Biol. 15, 4735-4744
75. Sauer, F., Fondell, J.D., Ohkuma, Y., Roeder, R.G., and Jäckle, H. (1995) Control of transcription by Krüppel through interactions with TFIIB and TFIIEβ. Nature 375, 162-164
76. Sakurai, H., Kim, Y.-J., Ohishi, T., Kornberg, R.D., and Fukasawa, T. (1996) The yeast GAL11 protein binds to the transcription factor IIE through GAL11 regions essential for its in vivo function. Proc. Natl. Acad. Sci. USA 93, 9488-9492
77. Kojima, S., Kobayashi, A., Gotoh, O., Ohkuma, Y., Fujii-Kuriyama, Y., and Sogawa, K. (1997) Transcriptional activation domain of human BTEB2, a GC box binding factor. J. Biochem. 121, 389-396
78. Martin, M.L., Lieberman, P.M., and Curran, T. (1996) Fos-Jun dimerization promotes interaction of the basic region with TFIIE-34 and TFIIF. Mol. Cell. Biol. 16, 2110-2118
79. 1180 with other TAFs and with general transcription factors. Proc. Natl. Acad. Sci. USA 92, 8195-8199