Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF

Molecular Cell

Volumn 2, Issue 3, 1998, Pages 341-351

  Robert, François ^a   Douziech, Maxime ^a   Forget, Diane ^a   Egly, Jean Marc ^b   Greenblatt, Jack ^c   Burton, Zachary F ^d   Coulombe, Benoit ^a  

^a UNIVERSITÉ DE SHERBROOKE   (Canada)

^b INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^c UNIVERSITY OF TORONTO   (Canada)

^d Michigan State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CROSS LINKING REAGENT; RECOMBINANT PROTEIN; RNA POLYMERASE II; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR II; TRANSCRIPTION FACTOR TFIIF; VIRUS DNA;

ADENOVIRUS; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROMOTER REGION; PROTEIN CONFORMATION;

ADENOVIRIDAE; BASE SEQUENCE; BINDING SITES; CROSS-LINKING REAGENTS; DNA, VIRAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS (GENETICS); PROTEIN CONFORMATION; RECOMBINANT PROTEINS; RNA POLYMERASE II; TRANSCRIPTION FACTORS; TRANSCRIPTION FACTORS, TFII;

EID: 0032161845     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1097-2765(00)80278-6     Document Type: Article

References (66)

1. Bartholomew, B., Kassavetis, G.A., Braun, B.R., and Geiduschek, E.P. (1990). The subunit structure of Saccharomyces cerevisiae transcription factor IIIC probed with a novel photocrosslinking reagent. EMBO J. 7, 2197-2205.
2. Buratowski, S., Sopta, M., Greenblatt, J., and Sharp, P.A. (1991). RNA polymerase II-associated proteins are required for a DNA conformation change in the transcription initiation complex. Proc. Natl. Acad. Sci. USA 88, 7509-7513.
3. 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.
4. Burke, T.W., and Kadonaga, J.T. (1997). The downstream core promoter element, DPE, is conserved from Drosophila to human and is recognized by TAFII60 of Drosophila. Genes Dev. 11, 3020-3031.
5. Burley, S.K., and Roeder, R.G. (1996). Biochemistry and structural biology of transcription factor IID (TFIID). Annu. Rev. Biochem. 65, 769-799.
6. 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.
7. Chen, J.L., Donatella Attardi, L., Verrijzer, C.P., Yokomori, K., and Tjian, R. (1994). Assembly of recombinant TFIID reveals differential coactivator requirements for distinct transcriptional activators. Cell 79, 93-105.
8. Chiang, C.M., and Roeder, R.G. (1995). Cloning of an intrinsic human TFIID subunit that interacts with multiple transcriptional activators. Science 267, 531-536.
9. Chiang, C.M., Ge, H., Wang, Z., Hoffmann, A., and Roeder, R.G. (1993). Unique TATA-binding protein-containing complexes and cofactors involved in transcription by RNA polymerases II and III. EMBO J. 12, 2749-2762.
10. 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.
11. Conaway, J.W., and Conaway, R.C. (1990). An RNA polymerase II transcription factor shares functional properties with Escherichia coli σ70. Science 248, 1550-1553.
12. Conaway, R.C., and Conaway, J.W. (1993). General initiation factors for RNA polymerase II. Annu. Rev. Biochem. 62, 161-190.
13. 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.
14. 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.
15. 32 at the groE promoter. J. Mol. Biol. 210, 521-530.
16. 2+ binding and its structural consequences at the transcription start site. Biochemistry 34, 15624-15632.
17. Darst, S.A., Edwards, A.M., Kubalek, E.W., and Kornberg, R.D. (1991). Three-dimensional structure of yeast RNA polymerase II at 16 Å resolution. Cell 66, 121-128.
18. Darst, S.A., Kubalek, E.W., and Kornberg, R.D. (1989). Three-dimensional Escherichia coli RNA polymerase holoenzyme determined by electron crystallography. Nature 340, 730-732.
19. II100 are required for functional interaction with transcription factor TFIIFβ (RAP30) and incorporation into the TFIID complex. EMBO J. 15, 3702-3712.
20. Fang, S.M., and Burton, Z.F. (1996). RNA polymerase II-associated protein (RAP) 74 binds transcription factor (TF) IIB and blocks TFIIB-RAP30 binding. J. Biol. Chem. 271, 11703-11709.
21. Flores, O., Maldonado, E., and Reinberg, D. (1989). Factors involved in specific transcription by mammalian RNA polymerase II. Factors IIE and IIF independently interact with RNA polymerase II. J. Biol. Chem. 264, 8913-8921.
22. 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.
23. 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.
24. 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.
25. Garrett, K.P., Serizawa, H., Hanley, J.P., Bradsher, J.N., Tsuboi, A., Arai, N., Yokota, T., Arai, K., Conaway, R.C., and Conaway, J.W. (1992). The carboxyl terminus of RAP30 is similar in sequence to region 4 of bacterial sigma factors and is required for function. J. Biol. Chem. 267, 23942-23949.
26. Gérard, M., Fisher, 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.
27. Gong, D.W., Hashimoto, S., Wada, K., Roeder, R.G., Nakatani, Y., and Horikoshi, M. (1992). Imperfect conservation of a sigma factor-like subregion in Xenopus general transcription factor RAP30. Nucleic Acids Res. 20, 6414.
28. Goodrich, J.A., and Tjian, R. (1994). TBP-TAF complexes: selectivity factors for eukaryotic transcription. Curr. Opin. Cell Biol. 6, 403-409.
29. Greenblatt, J. (1997). RNA polymerase II holoenzyme and transcriptional regulation. Curr. Opin. Cell Biol. 9, 310-319.
30. Ha, I., Roberts, S., Maldonado, E., Sun, X., Kim, L.U., Green, M., and Reinberg, D. (1993). Multiple functional domains of human transcription factor IIB: distinct interactions with two general transcription factors and RNA polymerase II. Genes Dev. 7, 1021-1032.
31. Hoffmann, A., Oelgeschlager, T., and Roeder, R.G. (1997). Considerations of transcriptional control mechanisms: do TFIID-core promoter complexes recapitulate nucleosome-like functions? Proc. Natl. Acad. Sci. USA 94, 8928-8935.
32. 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.
33. 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.
34. II30 is present in a distinct TFIID complex and is required for transcriptional activation by the estrogen receptor. Cell 79, 107-117.
35. Killeen, 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.
36. 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 pre-initiation complex. Proc. Natl. Acad. Sci. USA 94, 12268-12273.
37. Lagrange, T., Kim, T.-K., Orphanides, G., 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.
38. 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.
39. 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.
40. Malik, S., Guermah, M., and Roeder, R.G. (1998). A dynamic model for PC4 coactivator function in RNA polymerase II transcription. Proc. Natl. Acad. Sci. USA 95, 2192-2197.
41. Maxon, M.E., Goodrich, J.A., and Tjian, R. (1994). Transcription factor IIE binds preferentially to RNA polymerase IIa and recruits TFIIH: a model for promoter clearance. Genes Dev. 8, 515-524.
42. McCracken, S., and Greenblatt, J. (1991). Related RNA polymerase-binding regions in human RAP30/74 and Escherichia coli σ70. Science 253, 900-902.
43. Meyer-Almes, F.J., Heumann, H., and Porschke, D. (1994). The structure of the RNA polymerase-promoter complex. DNA-bending-angle by quantitative electrooptics. J. Mol. Biol. 236, 1-6.
44. Moqtaderi, Z., Bai, Y., Poon, D., Weil, P.A., and Struhl, K. (1996). TBP-associated factors are not generally required for transcriptional activation in yeast. Nature 383, 188-191.
45. Oelgeschlager, T., Chiang, C.M., and Roeder, R.G. (1996). Topology and reorganization of a human TFIID-promoter complex. Nature 382, 735-738.
46. Orphanides, G., Lagrange, T., and Reinberg, D. (1996). The general transcription factors of RNA polymerase II. Genes Dev. 10, 2657-2683.
47. 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.
48. Parvin, J.D., Timmers, H.T.M., and Sharp, P.A. (1992). Promoter specificity of basal transcription factors. Cell 68, 1135-1144.
49. Polyakov, A., Severinova, E., and Darst, S.A. (1995). Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell 83, 365-373.
50. 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.
51. Ruppert, S., and Tjian, R. (1995). Human TAFII250 interacts with RAP74: implications for RNA polymerase II initiation. Genes Dev. 9, 2747-2755.
52. Schickor, P., Metzger, W., Werel, W., Lederer, H., and Neumann, H. (1990). Topography of intermediates in transcription initiation of E. coli. EMBO J. 9, 2215-2220.
53. Smale, S.T., Schmidt, M.C., Berk, A.J., and Baltimore, D. (1990). Transcriptional activation by Sp1 as directed throught TATA or initiator: specific requirement for mammalian transcription factor IID. Proc. Natl. Acad. Sci. USA 87, 4509-4513.
54. 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.
55. Sopta, M., Burton, Z.F., and Greenblatt, J. (1989). Structure and associated DNA-helicase activity of a general transcription initiation factor that binds to RNA polymerase II. Nature 341, 410-414.
56. Tan, S., Aso, T., Conaway, R.C., and Conaway, J.W. (1994a). Roles for both the RAP30 and RAP74 subunits of transcription factor IIF in transcription initiation and elongation by RNA polymerase II. J. Biol. Chem. 269, 25684-25691.
57. Tan, S., Garrett, K.P., Conaway, R.C., and Conaway, J.W. (1994b). Cryptic DNA-binding domain in the C terminus of RNA polymerase II general transcription factor RAP30. Proc. Natl. Acad. Sci. USA 91, 9808-9812.
58. Tan, S., Conaway, R.C., and Conaway, J.W. (1995). Dissection of transcription factor TFIIF functional domains required for initiation and elongation. Proc. Natl. Acad. Sci. USA 92, 6042-6046.
59. Tang, H., Sun, X., Reinberg, D., and Ebright, R.H. (1996). Protein-protein interactions in eukaryotic transcription initiation: structure of the pre-initiation complex. Proc. Natl. Acad. Sci. USA 93, 1119-1124.
60. Travers, A.A. (1990). Why bend DNA? Cell 60, 177-180.
61. Verrijzer, C.P., and Tjian, R. (1996). TAFs mediate transcriptional activation and promoter selectivity. Trends Biochem. Sci. 21, 338-342.
62. Verrijzer, C.P., Yokomori, K., Chen, J.L., and Tjian, R. (1994). Drosophila TAFII150: similarity to yeast gene TSM-1 and specific binding to core promoter DNA. Science 264, 933-941.
63. Verrijzer, C.P., Chen, J.-L., Yokomori, K., and Tjian, R. (1995). Binding of TAFs to core elements directs promoter selectivity by RNA polymerase II. Cell 81, 1115-1125.
64. Walker, S.S., Reese, J.C., Apone, L.M., and Green, M.R. (1996). Transcription activation in cells lacking TAFIIs. Nature 383, 185-188.
65. 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.
66. Zinkel, S.A., and Crothers, D.M. (1991). Catabolite activator protein-induced DNA bending in transcription initiation. J. Mol. Biol. 279, 201-215.