DNA bending and wrapping around RNA polymerase: A 'revolutionary' model describing transcriptional mechanisms

Microbiology and Molecular Biology Reviews

Volumn 63, Issue 2, 1999, Pages 457-478

  Coulombe, Benoit ^a   Burton, Zachary F ^b  

^a UNIVERSITÉ DE SHERBROOKE   (Canada)

^b Michigan State University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; CURVED DNA; DNA HOMOLOG; RNA POLYMERASE; RNA POLYMERASE II; TRANSCRIPTION FACTOR;

CONFORMATION; DNA HELIX; ENZYME ACTIVE SITE; ESCHERICHIA COLI; ISOMERISM; MOLECULAR MODEL; NONHUMAN; PROKARYOTE; REVIEW; RNA TRANSLATION; SEQUENCE HOMOLOGY;

EID: 0033032415     PISSN: 10922172     EISSN: None     Source Type: Journal    
DOI: 10.1128/mmbr.63.2.457-478.1999     Document Type: Review

References (169)

1. Amouyal, M., and H. Buc. 1987. Topological unwinding of strong and weak promoters by RNA polymerase. A comparison between the lac wild-type and the UV5 sites of E. coli. J. Mol. Biol. 195:795-808.
2. II130 and mediates long-range activation of the α-and β-globin gene loci in an erythroid cell line. Proc. Natl. Acad. Sci. USA 94:10051-10056.
3. Aso, T., J. W. Conaway, and R. C. Conaway. 1995. The RNA polymerase II elongation complex. FASEB J. 9:1419-1428.
4. Asturias, F. J., G. D. Meredith, C. L. Poglitsch, and R. D. Kornberg. 1997. Two conformations of RNA polymerase II revealed by electron crystallography. J. Mol. Biol. 272:536-540.
5. Bengal, E., O. Flores, A. Krauskopf, D. Reinberg, and Y. Aloni. 1991. Role of the mammalian transcription factors IIF, IIS, and IIX during elongation by RNA polymerase II. Mol. Cell. Biol. 11:1195-1206.
6. Borukhov, S., K. Severinov, M. Kashlev, A. Lebedev, I. Bass, G. C. Rowland, P. P. Lim, R. E. Glass, V. Nikiforov, and A. Goldfarb. 1991. Mapping of trypsin cleavage and antibody-binding sites and delineation of a dispensable domain in the β subunit of E. coli RNA polymerase. J. Biol. Chem. 266:23921-23926.
7. Bradsher, J. N., K. W. Jackson, R. C. Conaway, and J. W. Conaway. 1993. RNA polymerase II transcription factor SIII. I. Identification, purification, and properties. J. Biol. Chem. 268:25587-25593.
8. Braun, B. R., B. Bartholomew, G. A. Kassavetis, and E. P. Geiduschek. 1992. Topography of transcription factor complexes on the S. cerevisiae 5 S RNA gene. J. Mol. Biol. 228:1063-1077.
9. Buc, H., and W. R. McClure. 1985. Kinetics of open complex formation between E. coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps. Biochemistry 24:2712-2723.
10. II60 of Drosophila. Genes Dev. 11:3020-3031.
11. Burke, T. W., and J. T. Kadonaga. 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.
12. Burley, S. K., and R. G. Roeder. 1996. Biochemistry and structural biology of transcription factor IID (TFIID). Annu. Rev. Biochem. 65:769-799.
13. Busby, S., and R. H. Ebright. 1997. Transcription activation at class II CAP-dependent promoters. Mol. Microbiol. 23:853-859.
14. Carey, M. 1998. The enhanceosome and transcriptional synergy. Cell 92: 5-8.
15. Carpousis, A. J., and J. D. Gralla. 1985. Interaction of RNA polymerase with lac UV5 promoter DNA during mRNA initiation and elongation. Foot-printing, methylation, and rifampicin-sensitivity changes accompanying transcription initiation. J. Mol. Biol. 183:165-177.
16. Chen, J. L., L. D. Attardi, C. P. Verrijzer, K. Yokomori, and R. Tjian. 1994. Assembly of recombinant TFIID reveals differential coactivator requirements for distinct transcriptional activators. Cell 79:93-105.
17. Chi, T., P. Lieberman, K. Ellwood, and M. Carey. 1995. A general mechanism for transcriptional synergy by eukaryotic activators. Nature 377:254-257.
18. Chiang, C. M., H. Ge, Z. Wang, A. Hoffmann, and R. G. Roeder. 1993. Unique TATA-binding protein-containing complexes and cofactors involved in transcription by RNA polymerases II and III. EMBO J. 12:2749-2762.
19. Chiang, C. M., and R. G. Roeder. 1995. Cloning of an intrinsic human TFIID subunit that interacts with multiple transcriptional activators. Science 267:531-536.
20. Conaway, J. W., and R. C. Conaway. 1989. A multisubunit transcription factor essential for accurate initiation by RNA polymerase II. J. Biol. Chem. 264:2357-2362.
21. 70. Science 248: 1550-1553.
22. Coulombe, B., J. Li, and J. Greenblatt. 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.
23. 32 at the groE promoter. J. Mol. Biol. 210:521-530.
24. 2+ binding and its structural consequences at the transcription start site. Biochemistry 34:15624-15632.
25. Crothers, D. M., and T. A. Steitz. 1992. Transcriptional activation by E. coli CAP protein, p. 501-534. In S. L. McKnight and K. R. Yamamoto (ed.), Transcriptional regulation, vol. 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
26. Darst, S. A., A. M. Edwards, E. W. Kubalek, and R. D. Kornberg. 1991. Three-dimensional structure of yeast RNA polymerase II at 16 angstrom resolution. Cell 66:121-129.
27. Darst, S. A., E. W. Kubalek, and R. D. Kornberg. 1989. Three-dimensional structure of E. coli RNA polymerase holoenzyme determined by electron crystallography. Nature 340:730-732.
28. II250 is a bipartite protein kinase that phosphorylates the base transcription factor RAP74. Cell 84: 781-790.
29. Dove, S. L., and A. Hochschild. 1998. Conversion of the ω subunit of E. coli RNA polymerase into a transcriptional activator or an activation target. Genes Dev. 12:745-754.
30. Dove, S. L., J. K. Joung, and A. Hochschild. 1997. Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature 386:627-630.
31. II100 are required for functional interaction with transcription factor TFIIF β (RAP30) and incorporation into the TFIID complex. EMBO J. 15:3702-3712.
32. Duval-Valentin, G., and R. Ehrlich. 1986. Interaction between E. coli RNA polymerase and the tetR promoter from pSC101: homologies and differences with other E. coli promoter systems from close contact point studies. Nucleic Acids Res. 14:1967-1983.
33. Dvir, A., R. C. Conaway, and J. W. Conaway. 1997. A role for TFIIH in controlling the activity of early RNA polymerase II elongation complexes. Proc. Natl. Acad. Sci. USA 94:9006-9010.
34. Dvir, A., S. Tan, J. W. Conaway, and R. C. Conaway. 1997. Promoter escape by RNA polymerase II. Formation of an escape-competent transcriptional intermediate is a prerequisite for exit of polymerase from the promoter. J. Biol. Chem. 272:28175-28178.
35. Eichenberger, P., S. Dethiollaz, H. Buc, and J. Geiselmann. 1997. Structural kinetics of transcription activation at the malT promoter of E. coli by UV laser footprinting. Proc. Natl. Acad. Sci. USA 94:9022-9027.
36. Erie, D. A., O. Hajiseyedjavadi, M. C. Young, and P. H. von Hippel. 1993. Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription. Science 262:867-873.
37. Finkel, S. E., and R. C. Johnson. 1992. The Fis protein: it's not just for DNA inversion anymore. Mol. Microbiol. 6:3257-3265.
38. Flores, O., I. Ha, and D. Reinberg. 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.
39. Forget, D., F. Robert, G. Grondin, Z. F. Burton, J. Greenblatt, and B. Coulombe. 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.
40. Gaal, T., W. Ross, E. E. Blatter, H. Tang, X. Jia, V. V. Krishnan, N. Assa-Munt, R. H. Ebright, and R. L. Gourse. 1996 DNA-binding determinants of the a subunit of RNA polymerase: novel DNA-binding domain architecture. Genes Dev. 10:16-26.
41. Gamper, H. B., and J. E. Hearst. 1982. A topological model for transcription based on unwinding angle analysis of E. coli RNA polymerase binary, initiation and ternary complexes. Cell 29:81-90.
42. Garrett, K. P., H. Serizawa, J. P. Hanley, J. N. Bradsher, A. Tsuboi, N. Arai, T. Yokota, K. Arai, R. C. Conaway, and J. W. Conaway. 1992. The carboxyl terminus of RAP30 is similar in sequence to region 4 of bacterial σ factors and is required for function. J. Biol. Chem. 267:23942-23949.
43. Goodrich, J. A., and R. Tjian. 1994. TBP-TAF complexes: selectivity factors for eukaryotic transcription. Curr. Opin. Cell Biol. 6:403-409.
44. Goosen, N., and P. van de Putte. 1995. The regulation of transcription initiation by integration host factor. Mol. Microbiol. 16:1-7.
45. Grachev, M. A., E. A. Lukhtanov, A. A. Mustaev, E. F. Zaychikov, M. N. Abdukayumov, I. V. Rabinov, V. I. Richter, Y. S. Skoblov, and P. G. Chistyakov. 1989. Studies of the functional topography of E. coli RNA polymerase. A method for localization of the sites of affinity labelling. Eur. J. Biochem. 180:577-585.
46. Greenblatt, J. 1997. RNA polymerase II holoenzyme and transcriptional regulation. Curr. Opin. Cell Biol. 9:310-319.
47. Groft, C. M., S. N. Uljon, R. Wang, and M. H. Werner. 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.
48. Gross, C. A., M. Lonetto, and R. Losick. 1992. Bacterial σ factors, p. 129-176. In S. L. McKnight and K. R. Yamamoto (ed.), Transcriptional regulation, vol. 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
49. Gu, W., and D. Reines. 1995. Variation in the size of nascent RNA cleavage products as a function of transcript length and elongation competence. J. Biol. Chem. 270:30441-30447.
50. Hampsey, M. 1998. Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. Mol. Biol. Rev. 62:465-503.
51. Hampsey, M., and D. Reinberg. 1997. Transcription: why are TAFs essential? Curr. Biol. 7:R44-R46.
52. RM promoter. J. Mol. Biol. 157:493-525.
53. Helmann, J. D. 1994. Bacterial σ factors, p. 1-18. In R. C. Conaway and J. W. Conaway (ed.), Transcription: mechanisms and regulation. Raven Press, New York, N.Y.
54. Heyduk, T., E. Heyduk, K. Severinov, H. Tang, and R. H. Ebright. 1996. Determinants of RNA polymerase a subunit for interaction with β, β′, and σ subunits: hydroxyl-radical protein footprinting. Proc. Natl. Acad. Sci. USA 93:10162-10166.
55. IIs and with general transcription factors. Proc. Natl. Acad. Sci. USA 92:8195-8199.
56. Hochschild, A., and S. L. Dove. 1998. Protein-protein contacts that activate and repress prokaryotic transcription. Cell 92:597-600.
57. Hoffmann, A., C. M. Chiang, T. Oelgeschlager, X. Xie, S. K. Burley, Y. Nakatani, and R. G. Roeder. 1996. A histone octamer-like structure within TFIID. Nature 380:356-359.
58. Hoffmann, A., T. Oelgeschlager, and R. G. Roeder. 1997. Considerations of transcriptional control mechanisms: do TFIID-core promoter complexes recapitulate nucleosome-like functions? Proc. Natl. Acad. Sci. USA 94: 8928-8935.
59. Holstege, F. C., D. Tantin, M. Carey, P. C. van der Vliet, and H. T. Timmers. 1995. The requirement for the basal transcription factor IIE is determined by the helical stability of promoter DNA. EMBO J. 14:810-819.
60. Horikoshi, M., T. Hai, Y. S. Lin, M. R. Green, and R. G. Roeder. 1988. Transcription factor ATF interacts with the TATA factor to facilitate establishment of a preinitiation complex. Cell 54:1033-1042.
61. Ishihama, A. 1981. Subunit of assembly of E. coli RNA polymerase. Adv. Biophys. 14:1-35.
62. Ishihama, A., and K. Ito. 1972. Subunits of RNA polymerase in function and structure. II. Reconstitution of E. coli RNA polymerase from isolated subunits. J. Mol. Biol. 72:111-123.
63. Izban, M. G., and D. S. Luse. 1992. Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates. J. Biol. Chem. 267:13647-13655.
64. Izban, M. G., and D. S. Luse. 1993. The increment of SII-facilitated transcript cleavage varies dramatically between elongation competent and incompetent RNA polymerase II ternary complexes. J. Biol. Chem. 268: 12974-12985.
65. Izban, M. G., and D. S. Luse. 1992. The RNA polymerase II ternary complex cleaves the nascent transcript in a 3′→5′ direction in the presence of elongation factor SII. Genes Dev. 6:1342-1356.
66. Izban, M. G., and D. S. Luse. 1993. SII-facilitated transcript cleavage in RNA polymerase II complexes stalled early after initiation occurs in primarily dinucleotide increments. J. Biol. Chem. 268:12964-12973.
67. II30 is present in a distinct TFIID complex and is required for transcriptional activation by the estrogen receptor. Cell 79:107-117.
68. Jeon, Y. H., T. Negishi, M. Shirakawa, T. Yamazaki, N. Fujita, A. Ishihama, and Y. Kyogoku. 1995. Solution structure of the activator contact domain of the RNA polymerase α subunit. Science 270:1495-1497.
69. Jin, D. J., and C. A. Gross. 1988. Mapping and sequencing of mutations in the E. coli rpoB gene that lead to rifampicin resistance. J. Mol. Biol. 202:45-58.
70. m for purine nucleotides during transcription elongation. J. Biol. Chem. 266:14478-14785.
71. Kaufmann, J., C. P. Verrijzer, J. Shao, and S. T. Smale. 1996. CIF, an essential cofactor for TFIID-dependent initiator function. Genes Dev. 10: 873-886.
72. Killeen, M. T., and J. F. Greenblalt. 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.
73. Kim, J. L., D. B. Nikolov, and S. K. Burley. 1993. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365:520-527.
74. Kim, T. K., T. Lagrange, Y. H. Wang, J. D. Griffith, D. Reinberg, and R. H. Ebright. 1997. Trajectory of DNA in the RNA polymerase II transcription preinitiation complex. Proc. Natl. Acad. Sci. USA 94:12268-12273.
75. Kim, Y., J. H. Geiger, S. Hahn, and P. B. Sigler. 1993. Crystal structure of a yeast TBP/TATA-box complex. Nature 365:512-520.
76. Kohlstaedt, L. A., J. Wang, J. M. Friedman, P. A. Rice, and T. A. Steitz. 1992. Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256:1783-1790.
77. Kovacic, R. T. 1987. The 0°C closed complexes between E. coli RNA polymerase and two promoters, T7-A3 and lacUVS. J. Biol. Chem. 262: 13654-13661.
78. Lagrange, T., A. N. Kapanidis, H. Tang, D. Reinberg, and R. H. Ebright. 1998. New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes Dev. 12:34-44.
79. Lagrange, T., T. K. Kim, G. Orphanides, Y. W. Ebright, R. H. Ebright, and D. Reinberg. 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.
80. Landick, R., J. Stewart, and D. N. Lee. 1990. Amino acid changes in conserved regions of the β-subunit of E. coli RNA polymerase alter transcription pausing and termination. Genes Dev. 4:1623-1636.
81. Langer, D., J. Hain, P. Thuriaux, and W. Zillig. 1995. Transcription in archaea: similarity to that in eucarya. Proc. Natl. Acad. Sci. USA 92:5768-5772.
82. Lavigne, M., M. Herbert, A. Kolb, and H. Buc. 1992. Upstream curved sequences influence the initiation of transcription at the E. coli galactose operon. J. Mol. Biol. 224:293-306.
83. Lee, T. I., and R. A. Young. 1998. Regulation of gene expression by TBP-associated proteins. Genes Dev. 12:1398-1408.
84. Lei, L., D. Ren, A. Finkelstein, and Z. F. Burton. 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.
85. Lieberman, P. M., and A. J. Berk. 1994. A mechanism for TAFs in transcriptional activation: activation domain enhancement of TFIID-TFIIA-promoter DNA complex formation. Genes Dev. 8:995-1006.
86. II230 complex: protein mimicry of the minor groove surface of the TATA box unwound by TBP. Cell 94:573-583.
87. Lobo, S. M., and N. T. Hernandez. 1994. Transcription of snRNA genes by RNA polymerases II and III, p. 127-159. In R. C. Conaway and J. W. Conaway (ed.), Transcription: mechanisms and regulation. Raven Press, New York, N.Y.
88. 70 family: sequence conservation and evolutionary relationships. J. Bacteriol. 174:3843-3849.
89. Luger, K., A. W. Mader, R. K. Richmond, D. F. Sargent, and T. J. Richmond. 1997. Crystal structure of the nucleosome core particle at 2.8 angstrom resolution. Nature 389:251-260.
90. Malik, S., M. Guermah, and R. G. Roeder. 1998. A dynamic model for PC4 coactivator function in RNA polymerase II transcription. Proc. Natl. Acad. Sci. USA 95:2192-2197.
91. Markovtsov, V., A. Mustaev, and A. Goldfarb. 1996. Protein-RNA interactions in the active center of transcription elongation complex. Proc. Natl. Acad. Sci. USA 93:3221-3226.
92. II150-containing TFIID complex. Mol. Cell. Biol. 18:6571-6583.
93. Matsuzaki, H., G. A. Kassavetis, and E. P. Geiduschek. 1994. Analysis of RNA chain elongation and termination by S. cerevisiae RNA polymerase III. J. Mol. Biol. 235:1173-1192.
94. McClure, W. R., and C. L. Cech. 1978. On the mechanism of rifampicin inhibition of RNA synthesis. J. Biol. Chem. 253:8949-8956.
95. 70. Science 253:900-902.
96. Mecsas, J., D. W. Cowing, and C. A. Gross. 1991. Development of RNA polymerase-promoter contacts during open complex formation. J. Mol. Biol. 220:585-597.
97. Meier, T., P. Schickor, A. Wedel, L. Cellai, and H. Heumann. 1995. In vitro transcription close to the melting point of DNA: analysis of Thermotoga maritima: RNA polymerase-promoter complexes at 75°C using chemical probes. Nucleic Acids Res. 23:988-994.
98. Merkel, T. J., J. L. Dahl, R. H. Ebright, and R. J. Kadner. 1995 Transcription activation at the E. coli uhpT promoter by the catabolite gene activator protein. J. Bacteriol. 177:1712-1718.
99. Meyer-Almes, F. J., H. Heumann, and D. Porschke. 1994. The structure of the RNA polymerase-promoter complex. DNA-bending-angle by quantitative electrooptics. J. Mol. Biol. 236:1-6.
100. Moqtaderi, Z., Y. Bai, D. Poon, P. A. Weil, and K. Struhl. 1996. TBP-associated factors are not generally required for transcriptional activation in yeast. Nature 383:188-191.
101. II70. Nucleic Acids Res. 26:2899-2907.
102. Muskhelishvili, G., A. A. Travers, H. Heumann, and R. Kahmann. 1995. FIS and RNA polymerase holoenzyme form a specific nucleoprotein complex at a stable RNA promoter. EMBO J. 14:1446-1452.
103. Mustaev, A., M. Kashlev, J. Y. Lee, A. Polyakov, A. Lebedev, K. Zalenskaya, M. Grachev, A. Goldfarb, and V. Nikiforov. 1991. Mapping of the priming substrate contacts in the active center of E. coli RNA polymerase. J. Biol. Chem. 266:23927-23931.
104. Mustaev, A., M. Kozlov, V. Markovtsov, E. Zaychikov, L. Denissova, and A. Goldfarb. 1997. Modular organization of the catalytic center of RNA polymerase. Proc. Natl. Acad. Sci. USA 94:6641-6645.
105. Mustaev, A., E. Zaychikov, K. Severinov, M. Kashlev, A. Polyakov, V. Nikiforov, and A. Goldfarb. 1994. Topology of the RNA polymerase active center probed by chimeric rifampicin-nucleotide compounds. Proc. Natl. Acad. Sci. USA 91:12036-12040.
106. Nikolov, D. B., H. Chen, E. D. Halay, A. A. Usheva, K. Hisatake, D. K. Lee, R. G. Roeder, and S. K. Burley. 1995. Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature 377:119-129.
107. Niu, W., Y. Kim, G. Tau, T. Heyduk, and R. H. Ebright. 1996. Transcription activation at class II CAP-dependent promoters: two interactions between CAP and RNA polymerase. Cell 87:1123-1134.
108. Nudler, E., E. Avetissova, V. Markovtsov, and A. Goldfarb. 1996. Transcription processivity: protein-DNA interactions holding together the elongation complex. Science 273:211-217.
109. Nudler, E., I. Gusarov, E. Avetissova, M. Kozlov, and A. Goldfarb. 1998. Spatial organization of transcription elongation complex in E. coli. Science 281:424-428.
110. Nudler, E., A. Mustaev, E. Lukhtanov, and A. Goldfarb. 1997. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 89:33-41.
111. Oelgeschlager, T., C. M. Chiang, and R. G. Roeder. 1996. Topology and reorganization of a human TFIID-promoter complex. Nature 382:735-738.
112. IIs. Mol. Cell 1:925-931.
113. Olave, I., D. Reinberg, and L. D. Vales 1998. The mammalian transcriptional repressor RBP (CBF1) targets TFIID and TFIIA to prevent activated transcription. Genes Dev. 12:1621-1637.
114. Orphanides, G., T. Lagrange, and D. Reinberg. 1996. The general transcription factors of RNA polymerase II. Genes Dev. 10:2657-2683.
115. Pan, G., and J. Greenblatt. 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.
116. Parvin, J. D., B. M. Shykind, R. E. Meyers, J. Kim, and P. A. Sharp. 1994. Multiple sets of basal factors initiate transcription by RNA polymerase II. J. Biol. Chem. 269:18414-18421.
117. Polyakov, A., E. Severinova, and S. A. Darst. 1995. Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell 83:365-373.
118. Price, D. H., A. E. Sluder, and A. L. Greenleaf. 1989. Dynamic interaction between a Drosophila transcription factor and RNA polymerase II. Mol. Cell. Biol. 9:1465-1475.
119. Ptashne, M., and A. Gann. 1997. Transcriptional activation by recruitment. Nature 386:569-577.
120. Qureshi, S. A., P. Baumann, T. Rowlands, B. Khoo, and S. P. Jackson. 1995. Cloning and functional analysis of the TATA binding protein from Sulfolobus shibatae. Nucleic Acids Res. 23:1775-1781.
121. Qureshi, S. A., S. D. Bell, and S. P. Jackson. 1997. Factor requirements for transcription in the Archaeon Sulfolobus shibatae. EMBO J. 16:2927-2936.
122. Qureshi, S. A., and S. P. Jackson. 1998. Sequence-specific DNA binding by the S. shibatae TFIIB homolog. TFB. and its effect on promoter strength. Mol. Cell 1:389-400.
123. Qureshi, S. A., B. Khoo, P. Baumann, and S. P. Jackson. 1995. Molecular cloning of the transcription factor TFIIB homolog from Sulfolobus shibatae. Proc. Natl. Acad. Sci. USA 92:6077-6081.
124. Rees, W. A., R. W. Keller, J. P. Vesenka, G. Yang, and C. Bustamante. 1993. Evidence of DNA bending in transcription complexes imaged by scanning force microscopy. Science 260:1646-1649.
125. Reines, D. 1992. Elongation factor-dependent transcript shortening by template-engaged RNA polymerase II. J. Biol. Chem. 267:3795-3800.
126. Reines, D., J. W. Conaway, and R. C. Conaway. 1996. The RNA polymerase II general elongation factors. Trends Biochem. Sci. 21:351-355.
127. Reference deleted.
128. Reference deleted.
129. Robert, F., M. Douziech, D. Forget, J.-M. Egly, J. Greenblatt, Z. F. Burton, and B. Coulombe. 1998. Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF. Mol. Cell 2:341-351.
130. Robert, F., D. Forget, J. Li, J. Greenblatt, and B. Coulombe. 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.
131. R promoter interaction. Assignment of the kinetic steps corresponding to protein conformational change and DNA opening. J. Mol. Biol. 184:441-453.
132. Roy, A. L., H. Du, P. D. Gregor, C. D. Novina, E. Martinez, and R. G. Roeder. 1997. Cloning of an inr-and E-box-binding protein, TFII-I, that interacts physically and functionally with USF1. EMBO J. 16:7091-7104.
133. Rudd, M. D., M. G. Izban, and D. S. Luse. 1994. The active site of RNA polymerase II participates in transcript cleavage within arrested ternary complexes. Proc. Natl. Acad. Sci. USA 91:8057-8061.
134. Savery, N. J., G. S. Lloyd, M. Kainz, T. Gaal, W. Ross, R. H. Ebright, R. L. Gourse, and S. J. Busby. 1998. Transcription activation at class II CRP-dependent promoters: identification of determinants in the C-terminal domain of the RNA polymerase α subunit. EMBO J. 17:3439-3447.
135. Sawadogo, M., and R. G. Roeder. 1985. Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. Cell 43:165-175.
136. Schickor, P., W. Metzger, W. Werel, H. Lederer, and H. Heumann. 1990. Topography of intermediates in transcription initiation of E. coli. EMBO J. 9:2215-2220.
137. Schultz, S. C., G. C. Shields, and T. A. Steitz. 1991. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 253:1001-1007.
138. Sentenac, A., M. Riva, P. Thuriaux, J.-M. Buhler, I. Treich, C. Carles, M. Werner, A. Ruet, J. Huet, C. Mann, N. Chiannilkulchai, S. Stettler, and S. Mariotte. 1992. Yeast RNA polymerase subunits and genes, p. 27-54. In S. L. McKnight and K. R. Yamamoto (ed.), Transcriptional regulation, vol. 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y.
139. Severinov, K., D. Fenyo, E. Severinova, A. Mustaev, B. T. Chait, A. Goldfarb, and S. A. Darst. 1994. The σ subunit conserved region 3 is part of "5′-face" of active center of E. coli RNA polymerase. J. Biol. Chem. 269: 20826-20828.
140. Severinov, K., A. Mustaev, A. Kukarin, O. Muzzin, I. Bass, S. A. Darst, and A. Goldfarb. 1996. Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the β and β′ subunits of E. coli RNA polymerase. J. Biol. Chem. 271:27969-27974.
141. Severinov, K., A. Mustaev, E. Severinova, M. Kozlov, S. A. Darst, and A. Goldfarb. 1995. The β subunit Rif-cluster I is only angstroms away from the active center of E. coli RNA polymerase. J. Biol. Chem. 270(49):29428-29432.
142. Shilatifard, A., D. R. Duan, D. Haque, C. Florence, W. H. Schubach, J. W. Conaway, and R. C. Conaway. 1997. ELL2, a new member of an ELL family of RNA polymerase II elongation factors. Proc. Natl. Acad. Sci. USA 94: 3639-3643.
143. Shilatifard, A., D. Haque, R. C. Conaway, and J. W. Conaway. 1997. Structure and function of RNA polymerase II elongation factor ELL. Identification of two overlapping ELL functional domains that govern its interaction with polymerase and the ternary elongation complex. J. Biol. Chem. 272:22355-22363.
144. Shilatifard, A., W. S. Lane, K. W. Jackson, R. C. Conaway, and J. W. Conaway. 1996. An RNA polymerase II elongation factor encoded by the human ELL gene. Science 271:1873-1876.
145. Sidorenkov, I., N. Komissarova, and M. Kashlev. 1998. Crucial role of the RNA:DNA hybrid in the processivity of transcription. Mol. Cell 2:55-64.
146. Siebenlist, U. 1979. RNA polymerase unwinds an 11-base pair segment of a phage T7 promoter. Nature 279:651-652.
147. Siebenlist, U., R. B. Simpson, and W. Gilbert. 1980. E. coli RNA polymerase interacts homologously with two different promoters. Cell 20:269-281.
148. Smale, S. T. 1994. Core promoter architecture for eukaryotic protein-coding genes, p. 63-81. In R. C. Conaway and J. W. Conaway (ed.), Transcription: mechanisms and regulation. Raven Press, New York, N.Y.
149. Sopta, M., Z. F. Burton, and J. Greenblatt. 1989. Structure and associated DNA-helicase activity of a general transcription initiation factor that binds to RNA polymerase II. Nature 341:410-414.
150. Spassky, A., K. Kirkegaard, and H. Buc. 1985. Changes in the DNA structure of the lacUV5 promoter during formation of an open complex with E. coli RNA polymerase. Biochemistry 24:2723-2731.
151. Steitz, T. A., S. J. Smerdon, J. Jager, and C. M. Joyce. 1994. A unified polymerase mechanism for nonhomologous DNA and RNA polymerases. Science 266:2022-2025.
152. Svetlov, V., K. Nolan, and R. R. Burgess. 1998. Rpb3, stoichiometry and sequence determinants of the assembly into yeast RNA polymerase II in vivo. J. Biol. Chem. 273:10827-10830.
153. Tan, S., K. P. Garrett, R. C. Conaway, and J. W. Conaway. 1994. Cryptic DNA-binding domain in the C terminus of RNA polymerase II general transcription factor RAP30. Proc. Natl. Acad. Sci. USA 91:9808-9812.
154. Tansey, W. P., and W. Herr. 1997. TAFs: guilt by association? Cell 88: 729-732.
155. Thuillier, V., I. Brun, A. Sentenac, and M. Werner. 1996. Mutations in the α-amanitin conserved domain of the largest subunit of yeast RNA polymerase III affect pausing, RNA cleavage and transcriptional transitions. EMBO J. 15:618-629.
156. Travers, A. A. 1990. Why bend DNA? Cell 60:177-180.
157. Verrijzer, C. P., J. L. Chen, K. Yokomori, and R. Tjian. 1995. Binding of TAFs to core elements directs promoter selectivity by RNA polymerase II. Cell 81:1115-1125.
158. Verrijzer, C. P., and R. Tjian. 1996. TAFs mediate transcriptional activation and promoter selectivity. Trends Biochem. Sci. 21:338-342.
159. II150: similarity to yeast gene TSM-1 and specific binding to core promoter DNA. Science 264:933-941.
160. IIS. Nature 383:185-188.
161. Wang, D., and D. K. Hawley. 1993. Identification of a 3′⇒5′ exonuclease activity associated with human RNA polymerase II. Proc. Natl. Acad. Sci. USA 90:843-847.
162. Werner, M., N. Chaussivert, I. M. Willis, and A. Sentenac. 1993. Interaction between a complex of RNA polymerase III subunits and the 70-kDa component of transcription factor IIIB. J. Biol. Chem. 268:20721-20724.
163. II-containing complex without TBP in transcription by RNA polymerase II. Nature 393:187-191.
164. Woychik, N. A., and R. A. Young. 1994. Exploring RNA polymerase II structure and function, p. 227-242. In R. C. Conaway and J. W. Conaway (ed.), Transcription: mechanisms and regulation, vol. 3. Raven Press, New York, N.Y.
165. Zaychikov, E., L. Denissova, and H. Heumann. 1995. Translocation of the E. coli transcription complex observed in the registers 11 to 20: "jumping" of RNA polymerase and asymmetric expansion and contraction of the "transcription bubble." Proc. Natl. Acad. Sci. USA 92:1739-1743.
166. Zaychikov, E., E. Martin, L. Denissova, M. Kozlov, V. Markovtsov, M. Kashlev, H. Heumann, V. Nikiforov, A. Goldfarb, and A. Mustaev. 1996. Mapping of catalytic residues in the RNA polymerase active center. Science 273:107-109.
167. Zhang, G., and S. A. Darst. 1998. Structure of the E. coli RNA polymerase α subunit amino-terminal domain. Science 281:262-266.
168. Zhou, Q., P. M. Lieberman, T. G. Boyer, and A. J. Berk. 1992. Holo-TFIID supports transcriptional stimulation by diverse activators and from a TATA-less promoter. Genes Dev. 6:1964-1974.
169. Zhou, Y., T. J. Merkel, and R. H. Ebright. 1994. Characterization of the activating region of E. coli catabolite gene activator protein (CAP). II. Role at class I and class II CAP-dependent promoters. J. Mol. Biol. 243:603-610.