Structure and function of RNA polymerase II

Advances in Protein Chemistry

Volumn 67, Issue , 2004, Pages 1-42

  Cramer, Patrick ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA AMANITIN; ARCHAEAL RNA; BACTERIAL ENZYME; DNA; DNA DIRECTED RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE III; ELONGATION FACTOR; MESSENGER RNA; RNA POLYMERASE II;

CATALYSIS; DNA RNA HYBRIDIZATION; ENZYME STRUCTURE; GENETIC TRANSCRIPTION; HUMAN; METHANOCOCCUS JANNASCHII; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; RNA PROCESSING; RNA SYNTHESIS; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; THERMOCOCCUS; TRANSCRIPTION TERMINATION; X RAY CRYSTALLOGRAPHY;

ARCHAEA; BACTERIA (MICROORGANISMS); METHANOCALDOCOCCUS JANNASCHII; METHANOCOCCUS; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; THERMOCOCCUS;

EID: 1242273889     PISSN: 00653233     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-3233(04)67001-X     Document Type: Article

References (200)

1. Adelman, K., La Porta, A., Santangelo, T. J., Lis, J. T., Roberts, J. W., and Wang, M. D. (2002). Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior. Proc. Natl. Acad. Sci. USA 99(21), 13538-13543.
2. Albert, T., Mautner, J., Funk, J. O., Hortnagel, K., Pullner, A., and Eick, D. (1997). Nucleosomal structures of e-myc promoters with transcriptionally engaged RNA polymerase II. Mol. Cell. Biol. 17(8), 4363-4371.
3. Armache, K.-J., Kettenberger, H., and Cramer, P. (2003). Architecture of the initiation-competent 12-subunit RNA polymerase II. Proc. Natl. Acad. Sci. USA 100(12), 6964-6968.
4. Artsimovitch, I., and Landick, R. (2000). Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc. Natl. Acad. Sci. USA 97(13), 7090-7095.
5. Asturias, F. J., Meredith, G. D., Poglitsch, C. L., and Kornberg, R. D. (1997). Two conformations of RNA polymerase II revealed by electron crystallography. J. Mol. Biol. 272(4), 536-540.
6. Barabino, S. M., and Keller, W. (1999). Last but not least: regulated poly(A) tail formation. Cell 99(1), 9-11.
7. Baskaran, R., Chiang, G. G., Mysliwiec, T., Kruh, G. D., and Wang, J. Y. (1997). Tyrosine phosphorylation of RNA polymerase II carboxyl terminal domain by the Ab1 related gene product. J. Biol. Chem. 272(30), 18905-18909.
8. Beard, W. A., and Wilson, S. H. (2001). DNA lesion by pass polymerases open up. Structure (Camb) 9(9), 759-764.
9. Bell, S. D., and Jackson, S. P. (2001). Mechanism and regulation of transcription in archaea. Curr. Opin. Microbiol. 4(2), 208-213.
10. Bentley, D. (2002). The mRNA assembly line: transcription and processing machines in the same factory. Curr. Opin. Cell. Biol. 14(3), 336-342.
11. Bischler, N., Brino, L., Carles, C., Riva, M., Tschochner, H., Mallouh, V., and Schultz, P. (2002). Localization of the yeast RNA polymerase I-specific subunits. EMBO J. 21(15), 4136-4144.
12. Brautigam, C. A., and Steitz, T. A. (1998). Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr. Opin. Struct. Biol. 8(1), 54-63.
13. Buratowski, S. (1994). The basics of basal transcription by RNA polymerase II. Cell 77(1), 1-3.
14. Buratowski, S., Hahn, S., Guarente, L., and Sharp, P. A. (1989). Five intermediate complexes in transcription initiation by RNA polymerase II. Cell 56, 549-561.
15. Burke, T. W., Willy, P. J., Kutach, A. K., Butler, J. E., and Kadonaga, J. T. (1998). The DPE, a conserved downstream core promoter element that is functionally analogous to the TATA box. Cold Spring Harb. Symp. Quant. Biol. 63, 75-82.
16. Bushnell, D. A., Cramer, P., and Kornberg, R. D. (2001). Selenomethionine incorporation in Saccharomyces cerevisiae RNA polymerase II. Struct. Fold. Des. 9(1), R3-R9.
17. Bushnell, D. A., Cramer, P., and Kornberg, R. D. (2002). Structural basis of transcription: α-amanitin RNA polymerase II cocrystal at 2.8 A resolution. Proc. Natl. Acad. Sci. USA 99, 1218-1222.
18. Bushnell, D. A., and Kornberg, R. D. (2003). Complete 12-subunit RNA polymerase II at 4.1 Å resolution: implications for the initiation of transcription. Proc. Natl. Acad. Sci. USA 100(12), 6969-6972.
19. Cadena, D. L., and Dahmus, M. E. (1987). Messenger RNA synthesis in mammalian cells is catalyzed by the phosphorylated form of RNA polymerase II. J. Biol. Chem. 262(26), 12468-12474.
20. Cagas, P. M., and Corden, J. L. (1995). Structural studies of a synthetic peptide derived from the carboxyl-terminal domain of RNA polymerase II. Proteins 21(2), 149-160.
21. Chafin, D. R., Guo, H., and Price, D. H. (1995). Actions of α-amanitin during pyrophosphoryolysis and elongation by RNA polymerase II. J. Biol. Chem. 270, 19114-19119.
22. Chedin, S., Riva, M., Schultz, P., Sentenac, A., and Carles, C. (1998). The RNA cleavage activity of RNA polymerase III is mediated by an essential TFHS-like subunit and is important for transcription termination. Genes Dev. 12, 3857-3871.
23. Cho, H., Kim, T. K., Mancebo, H., Lane, W. S., Flores, O., and Reinberg, D. (1999). A protein phosphatase functions to recycle RNA polymerase II. Genes Dev. 13(12), 1540-1552.
24. Conaway, J. W., and Conaway, R. C. (1999). Transcription elongation and human disease. Annu. Rev. Biochem. 68, 301-319.
25. Cook, P. R. (1999). The organization of replication and transcription. Science 284(5421), 1790-1795.
26. Cox, J. M., Hayward, M. M., Sanchez, J. F., Gegnas, L. D., van der Zee, S., Dennis, J. H., Sigler, P. B., and Schepartz, A. (1997). Bidirectional binding of the TATA box binding protein to the TATA box. Proc. Natl. Acad. Sci. USA 94(25), 13475-13480.
27. Craighead, J. L., Chang, W. H., and Asturias, F. J. (2002). Structure of yeast RNA polymerase II in solution: implications for enzyme regulation and interaction with promoter DNA. Struct. Fold. Des. 10(8), 1117-1125.
28. Cramer, P. (2002a). Common structural features of nucleic acid polymerases. Bioessays 24, 724-729.
29. Cramer, P. (2002b). Multisubunit RNA polymerases. Curr. Op. Struct. Biol. 12, 89-97.
30. 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(5466), 640-649.
31. Cramer, P., Bushnell, D. A., and Kornberg, R. D. (2001). Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292(5523), 1863-1876.
32. Dahmus, M. E. (1996). Reversible phosphorylation of the C-terminal domain of RNA polymerase II. J. Biol. Chem. 271 (32), 19009-19012.
33. Darcy, T. J., Hausner, W., Awery, D. E., Edwards, A. M., Thomm, M., and Reeve, J. N. (1999). Methanobacterium thermoautotrophicum RNA polymerase and transcription in vitro. J. Bacteriol. 181 (14), 4424-4429.
34. Darst, S. A. (2001). Bacterial RNA polymerase. Curr. Opin. Struct. Biol. 11 (2), 155-162.
35. Darst, S. A., Edwards, A. M., Kubalek, E. W., and Kornberg, R. D. (1991a). Three-dimensional structure of yeast RNA polymerase II at 16 A resolution. Cell 66, 121-128.
36. Darst, S. A., Kubalek, E. W., Edwards, A. M., and Kornberg, R. D. (1991b). Two-dimensional and epitaxial crystallization of a mutant form of yeast RNA polymerase II. J. Mol. Biol. 221, 347-357.
37. Davenport, R.J., Wuite, G.J., Landick, R., and Bustamante, C. (2000). Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase. Science 287(5462), 2497-2500.
38. Davis, J. A., Takagi, Y., Kornberg, R. D., and Asturias, F. A. (2002). Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. Mol. Cell 10(2), 409-415.
39. del Rio-Portilla, F., Gaskell, A., Gilbert, D., Ladias, J. A., and Wagner, G. (1999). Solution structure of the hRPABC14.4 subunit of human RNA polymerases. Nat. Struct. Biol 6(11), 1039-1042.
40. Doublie, S., Sawaya, M. R., and Ellenberger, T. (1999). An open and closed case for all polymerases. Struct. Fold. Des. 7(2), R31-R35.
41. Doublie, S., Tabor, S., Long, A. M., Richardson, C. C., and Ellenberger, T. (1998). Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature 391, 251-258.
42. Dvir, A. (2002). Promoter escape by RNA polymerase II. Biochim. Biophys. Acta. 1577(2), 208-223.
43. Ebright, R. H. (1998). RNA polymerase-DNA interaction. Structures of intermediate, open, and elongation complexes. Cold Spring Harb. Symp. Quant. Biol. 63, 11-20.
44. Ebright, R. H. (2000). RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J. Mol. Biol. 304(5), 687-698.
45. Ederth, J., Artsimovitch, I., Isaksson, L. A., and Landick, R. (2002). The downstream DNAjaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing. J. Biol. Chem. 277(40), 37456-37463.
46. Edwards, A. M., Darst, S. A., Feaver, W. J., Thompson, N. E., Burgess, R. R., and Kornberg, R. D. (1990). Purification and lipid layer crystallization of yeast RNA polymerase II. Proc. Natl. Acad. Sci. USA 87, 2122-2126.
47. Edwards, A. M., Kane, C. M., Young, R. A., and Kornberg, R. D. (1991). Two dissociable subunits of yeast RNA polymerase II stimulate the initiation of transcription at a promoter in vitro. J. Biol. Chem. 266, 71-75.
48. Ellenberger, T., and Silvian, L. F. (2001). The anatomy of infidelity. Nat. Struct. Biol. 8(10), 827-828.
49. Erie, D. A. (2002). The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription. Biochim. Biophys. Acta. 1577(2), 224-239.
50. Ferri, M. L., Peyroche, G., Siaut, M., Lefebvre, O., Carles, C., Conesa, C., and Sentenac, A. (2000). A novel subunit of yeast RNA polymerase III interacts with the TFIIB-related domain of TFIIIB70. Mol. Cell. Biol. 20(2), 488-495.
51. Fiedler, U., and Marc Timmers, H. T. (2000). Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II. Bioessays 22(4), 316-326.
52. Fiedler, U., and Timmers, H. T. (2001). Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation. Nucleic Acids Res. 2706-2714.
53. Flores, A., Briand, J. F., Gadal, O., Andrau, J. C., Rubbi, L., Van Mullem, V., Boschiero, C., Goussot, M., Marck, C., Carles, C., Thuriaux, P., Sentenac, A., and Werner, M. (1999). A protein-protein interaction map of yeast RNA polymerase III. Proc. Natl. Acad. Sci. USA 96(14), 7815-7820.
54. Forde, N. R., Izhaky, D., Woodcock, G. R., Wuite, G. J., and Bustamante, C. (2002). Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase. Proc. Natl. Acad. Sci. USA 99(18), 11682-11687.
55. Franklin, M. C., Wang, J., and Steitz, T. A. (2001). Structure of the replicating complex of a pol alpha family DNA polymerase. Cell 105(5), 657-667.
56. Fu, J., Gerstein, M., David, P. R., Gnatt, A. L., Bushnell, D. A., Edwards, A. M., and Kornberg, R. D. (1998). Repeated tertiary fold of RNA polymerase II and implications for DNA binding. J. Mol. Biol. 280, 317-322.
57. 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.
58. Furter-Graves, E. M., Hall, B. D., and Furter, R. (1994). Role of a small RNA pol II subunit in TATA to transcription start site spacing. Nucleic Acids Res. 22 (23), 4932-4936.
59. Gnatt, A. (2002). Elongation by RNA polymerase II: structure function relationship. Biochim. Biophys. Acta. 1577(2), 175-190.
60. 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.
61. 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 Å resolution. Science 292(5523), 1876-1882.
62. Greenblatt, J. (1997). RNA polymerase II holoenzyme and transcriptional regulation. Curr. Opin. Cell. Biol. 9(3), 310-319.
63. Gu, W., Powell, W., Mote, J., and Reines, D. (1993). Nascent RNA cleavage by arrested RNA polymerase II does not require upstream translocation of the elongation complex on DNA. J. Biol. Chem. 268, 25604-25616.
64. Gu, W., and Reines, D. (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.
65. Gu, W., Wind, M., and Reines, D. (1996). Increased accommodation of nascent RNA in a product site on RNA polymerase II during arrest. Proc. Natl. Acad. Sci. USA 93, 6935-6940.
66. Hahn, S. (1998). Activation and the role of reinitiation in the control of transcription by RNA polymerase II. Cold spring Harb. Symp. Quant. Biol. 63, 181-188.
67. Hammell, C. M., Gross, S., Zenklusen, D., Health, C. V., Stutz, F., Moore, C., and Cole, C. N. (2002). Coupling of termination, 3′ processing, and mRNA export. Mol. Cell. Biol. 22(18), 6441-6457.
68. Hausner, W., Lange, U., and Musfeldt, M. (2000). Transcription factor S, a cleavage induction factor of the archaeal RNA polymerase. J. Biol. Chem. 275, 12393-12399.
69. Hirose, Y., and Manley, J. L. (2000). RNA polymerase II and the integration of nuclear events. Genes Dev. 14(12), 1415-1429.
70. Holstege, F. C. P., Fiedler, U., and Timmers, H. T. M. (1997). Three transitions in the RNA polymerase II transcription complex during initiation. EMBO J. 16, 7468-7480.
71. Hu, P., Wu, S., Sun, Y., Yuan, C. C., Kobayashi, R., Myers, M. P., and Hernandez, N. (2002). Characterization of human RNA polymerase III identifies orthologues for Saccharomyces cerevisiae RNA polymerase III subunits. Mol. Cell. Biol. 22(22), 8044-8055.
72. Hull, W. W., McKune, K., and Woychik, N. A. (1995). RNA polymerase II subunit RPB9 is required for accurate start site selection. Genes Dev. 9, 481-490.
73. Hunter, T. (1998). Prolyl isomerases and nuclear function. Cell 92(2), 141-143.
74. Izban, M. G., and Luse, D. S. (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.
75. Izban, M. G., and Luse, D. S. (1993a). The increment of SII facilitated transcript cleavage varies dramatically between elongation competent and incompetent RNA polymerase II ternary complexes. J. Biol. Chem. 268, 12874-12885.
76. Izban, M. G., and Luse, D. S. (1993). SII-facilitated transcript cleavage in RNA polymerase II complexes stalled early after initiation occurs in primarily dinucleotide increments. J. Biol. Chem. 268, 12864-12873.
77. Jager, J., and Pata, J. D. (1999). Getting a grip: polymerases and their substrate complexes. Curr. Opin. Struct. Biol. 9(1), 21-28.
78. Jensen, G. J., Meredith, G., Bushnell, D. A., and Kornberg, R. D. (1998). Structure of wild type yeast RNA polymerase 11 and location of Rpb4 and Rpb7. EMBO J. 17(8), 2353-2358.
79. Jeon, C-J., and Agarwal, K. (1996). Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS. Proc. Natl. Acad. Sci. USA 93, 13677-13682.
80. Jeon, C., Yoon, H., and Agarwal, K. (1994). The transcription factor TFIIS zinc ribbon dipeptide Asp-Glu is critical for stimulation of elongation and RNA cleavage by RNA polymerase II. Proc. Natl. Acad. Sci. USA 91, 9106-9110.
81. Jokerst, R. S., Weeks, J. R., Zehring, W. A., and Greenleaf, A. L. (1989). Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila. Mol. Gene Genet. 215, 266-275.
82. Kahl, B. F., Li, H., and Paule, M. R. (2000). DNA melting and promoter clearance by eukaryotic RNA polymerase I. J. Mol. Biol. 299(1), 75-89.
83. Kettenberger, H., Armache, K.-J., and Cramer, P. (2003). Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell 114(3), 347-357.
84. Khazak, V., Sadhale, P. P., Woychik, N. A., Brent, R., and Golemis, E. A. (1995). Human RNA polymerase II subunit hsRPB7 functions in yeast and influences stress survival and cell morphology. Mol. Biol. Cell 6(7), 759-775.
85. Killeen, M., Coulombe, B., and Greenblatt, J. (1992). Recombinant TBP, transcription factor IIB, and RAP30 are sufficient for promoter recognition by mammalian RNA polymerase II. J. Biol Chem. 267(14), 9463-9466.
86. 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.
87. Kim, T. K., Ebright, R. H., and Reinberg, D. (2000). Mechanism of ATP-dependent promoter melting by transcription factor IIH. Science 288(5470), 1418-1422.
88. Kim, Y., Geiger, J. H., Hahn, S., and Sigler, P. B. (1993). Crystal structure of a yeast TBP/TATA-box complex. Nature 365, 512-519.
89. Kimura, M., Suzuki, H., and Ishihama, A. (2002). Formation of a carboxy-terminal domain phosphatase (Fcp1)/TFIIF/RNA polymerase 11 (pol II) complex in Schizosaccharomyces pombe involves direct interaction between Fep1 and the Rpb4 subunit of pol II. Mol. Cell. Biol 22(5), 1577-1588.
90. Kireeva, M. L., Komissarova, N., Waugh, D. S., and Kashlev, M. (2000). The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. J. Biol. Chem. 275(9), 6530-6536.
91. 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(1), 55-62.
92. Kobor, M. S., and Greenblatt, J. (2002). Regulation of transcription elongation by phosphorylation. Biochim. Biophys. Acta. 1577(2), 261-275.
93. Komarnitsky, P., Cho, E.J., and Buratowski, S. (2000). Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14(19), 2452-2460.
94. Komissarova, N., and Kashlev, M. (1997a). RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA. J. Biol. Chem. 272, 15329-15338.
95. Komissarova, N., and Kashlev, M. (1997b). Transcription arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded. Proc. Natl. Acad. Sci. USA 94, 1755-1760.
96. Komissarova, N., and Kashlev, M. (1998). Functional topography of nascent RNA in elongation intermediates of RNA polymerase. Proc. Natl. Acad. Sci. USA 95, 14699-14704.
97. Kornberg, R. D. (1999). Eukaryotic transcriptional control. Trends Cell. Biol. 9(12), M46-M49.
98. Korzheva, N., Mustaev, A., Kozlov, M., Malhotra, A., Nikiforov, V., Goldfarb, A., and Darst, S. A. (2000). A structural model of transcription elongation. Science 289(5479), 619-625.
99. Korzheva, N., Mustaev, A., Nudler, E., Nikiforov, V., and Goldfarb, A. (1998). Mechanistic model of the elongation complex of Escherichia coli RNA polymerase. Cold Spring Harb. Symp. Quant. Biol. 63, 337-345.
100. Kosa, P., Ghosh, G., DeDecker, B. S., and Sigler, P. B. (1997). The 2.1-Å crystal structure of an archaeal preinitiation complex: TATA box binding protein/transcription factor (II)B core/TATA box. Proc. Natl. Acad. Sci. USA 94, 6042-6047.
101. Krapp, S., Kelly, G., Reischl, J., Weinzierl, R. O. J., and Matthews, S. (1998). Eukaryotic RNA polymerase subunit RPB8 is a new relative of the OB family. Nat. Struct. Biol. 5, 110-114.
102. Krumm, A., and Groudine, M. (1995). Tumor suppression and transcription elongation: the dire consequences of changing partners. Science 269(5229), 1400-1401.
103. Kugel, J. F., and Goodrich, J. A. (1998). Promoter escape limits the rate of RNA polymerase II transcription and is enhanced by TFIIE, TFIIH, and ATP on negatively supercoiled DNA. Proc. Natl. Acad. Sci. USA 95(16), 9232-9237.
104. Kugel, J. F., and Goodrich, J. A. (2000). A kinetic model for the early steps of RNA synthesis by human RNA polymerase II. J. Biol. Chem. 275 (51), 40483-40491.
105. Kugel, J. F., and Goodrich, J. A. (2002). Translocation after synthesis of a four nucleotide RNA commits RNA polymerase II to promoter escape. Mol. Cell. Biol. 22(3), 762-773.
106. Kuznedelov, K., Korzheva, N., Mustaev, A., and Severinov, K. (2002). Structure-based analysis of RNA polymerase function: the largest subunits rudder contributes critically to elongation complex stability and is not involved in the maintenance of RNA-DNA hybrid length. EMBO J. 21 (6), 1369-1378.
107. 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(1), 34-44.
108. Landick, R. (2001). RNA polymerase clamps down. Cell 105(5), 567-570.
109. Langer, D., Hain, J., Thuriaux, P., and Zillig, W. (1995). Transcription in archaea: similarity to that in eukarya. Proc. Natl. Acad. Sci. 92, 5768-5772.
110. Larkin, R. M., and Guilfoyle, T. J. (1998). Two small subunits in Arabidopsis RNA polymerase II are related to yeast RPB4 and RPB7 and interact with one another. J. Biol. Chem. 273(10), 5631-5637.
111. Leuther, K. K., Bushnell, D. A., and Kornberg, R. D. (1996). Two-dimensional crystallography of transcription factor IIB- and IIE-RNA polymerase II complexes: implications for start site selection and initiation complex formation. Cell 85, 773-779.
112. Li, B., Weber, J. A., Chen, Y., Greenleaf, A. L., and Gilmour, D. S. (1996). Analyses of promoter-proximal pausing by RNA polymerase II on the hsp 70 heat shock gene promoter in a Drosophila nuclear extract. Mol. Cell. Biol. 16(10), 5433-5443.
113. Li, Y., Korolev, S., and Waksman, G. (1998). Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. EMBO J. 17(24), 7514-7525.
114. Littlefield, O., Korkhin, Y., and Sigler, P. B. (1999). The structural basis for the oriented assembly of a TBP/TFB/promoter complex. Proc. Natl. Acad. Sci. USA 96(24), 13668-13673.
115. Mackereth, C. D., Arrowsmith, C. H., Edwards, A. M., and McIntosh, L. P. (2000). Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum Proc. Natl. Acad. Sci. USA 97(12), 6316-6321.
116. Magill, C. P., Jackson, S. P., and Bell, S. D. (2001). Identification of a conserved archaeal RNA polymerase subunit contacted by the basal transcription factor TFB. J. Biol. Chem. 276(50), 46693-46696.
117. Maniatis, T., and Reed, R. (2002). An extensive network of coupling among gene expression machines. Nature 416(6880), 499-506.
118. 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.
119. McKune, K., Richards, K. L., Edwards, A. M., Young, R. A., and Woychik, N. A. (1993). Rpb7, one of two dissociable subunits of yeast RNA polymerase II, is essential for cell viability. Yeast 9, 295-299.
120. Meredith, G. D., Chang, W.-H., Li, Y., Bushnell, D. A., Darst, S. A., and Kornberg, R. D. (1996). The C-terminal domain in the structure of RNA polymerase II. J. Mol. Biol. 258, 413-419.
121. Minakhin, L., Bhagat, S., Brunning, A., Campbell, E. A., Darst, S. A., Ebright, R. H., and Severinov, K. (2001). Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly. Proc. Natl. Acad. Sci. USA 98(3), 892-897.
122. 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(5571), 1285-1290.
123. Myer, V. E., and Young, R. A. (1998). RNA polymerase II holoenzymes and subcomplexes. J. Biol. Chem. 273(43), 27757-27760.
124. Nedialkov, Y. A., Gong, X. Q., Hovde, S. L., Yamaguchi, Y., Handa, H., Geiger, J. H., Yan, H., and Burton, Z. F. (2003). NTP-driven translocation by human RNA polymerase II. J. Biol. Chem. 278, 18303-18312.
125. 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.
126. Nudler, E. (1999). Transcription elongation: structural basis and mechanisms. J. Mol. Biol. 288(1), 1-12.
127. Nudler, E., Mustaev, A., Lukhtanov, E., and Goldfarb, A. (1997). The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 89, 38-41.
128. O'Brien, R., DeDecker, B., Fleming, K. G., Sigler, P. B., and Ladbury, J. E. (1998). The effects of salt on the TATA binding protein-DNA interaction from a hyperthermophilic archacon. J. Mol. Biol. 279(1), 117-125.
129. O'Brien, T., Hardin, S., Greenleaf, A., and Lis, J. T. (1994). Phosphorylation of RNA polymerase II C-terminal-domain and transcriptional elongation. Nature 370, 75-77.
130. Ohkuma, Y. (1997). Multiple functions of general transcription factors TFIIE and TFIIH in transcription. Possible points of regulation by trans acting factors. J. Biochem. 122, 481-489.
131. Opalka, N., Chlenov, M., Chacon, P., Rice, W. J., Wriggers, W., and Darst, S. A. (2003). Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell 114(3), 335-345.
132. Orlicky, S. M., Tran, P. T., Sayre, M. H., and Edwards, A. M. (2001). Dissociable Rpb4, Rpb7 subassembly of ma polymerase II binds to single-strand nucleic acid and mediates a post recruitment step in transcription initiation. J. Biol. Chem. 276(13), 10097-10102.
133. Orlova, M., Newlands, J., Das, A., Goldfarb, A., and Borukhov, S. (1995). Intrinsic transcript cleavage activity of RNA polymerase. Proc. Natl. Acad. Sci. USA 92(10), 4596-4600.
134. Orphanides, G., and Reinberg, D. (2000). RNA polymerase II elongation through chromatin. Nature 407 (6803), 471-475.
135. Orphanides, G., and Reinberg, D. (2002). A unified theory of gene expression. Cell 108(4), 439-451.
136. Ossipow, V., Iassan, J.-P., Nigg, E. A., and Schibler, U. (1995). A mammalian RNA polymerase II holoenzyme containing all components required for promoter-specific transcription initiation. Cell 83, 137-146.
137. Pal, M., and Luse, D. S. (2002). Strong natural pausing by RNA polymerase II within 10 bases of transcription start may result in repeated slippage and reextension of the nascent RNA. Mol. Cell. Biol. 22(1), 30-40.
138. Palangat, M., and Landick, R. (2001). Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II. J. Mol. Biol. 311(2), 265-282.
139. 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(48), 30101-30104.
140. Patel, P. H., and Loeb, L. A. (2001). Getting a grip on how DNA polymerases function. Nat. Struct. Biol. 8(8), 656-659.
141. Peyroche, G., Levillain, E., Siaut, M., Callebaut, I., Schultz, P., Sentenac, A., Riva, M., and Carles, C. (2002). The A14-A43 heterodimer subunit in yeast RNA pol I and their relationship to Rpb4-Rpb7 pol II subunits. Proc. Natl. Acad. Sci. USA 99(23), 14670-14675.
142. Peyroche, G., Milkereit, P., Bischler, N., Tschochner, H., Schultz, P., Sentenac, A., Carles, C., and Riva, M. (2000). The recruitment of RNA polymerase I on rDNA is mediated by the interaction of the A43 subunit with Rrn3. EMBO J. 19(20), 5473-5482.
143. 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.
144. Powell, W., Bartholomew, B, and Reines, D. (1996). Elongation factor SII contacts the 3′ end of RNA in the RNA polymerase II elongation complex. J. Biol. Chem. 271, 22301-22304.
145. Proudfoot, N. (2000). Connecting transcription to messenger RNA processing. Trends Biochem. Sci. 25(6), 290-293.
146. Proudfoot, N. J., Furger, A., and Dye, M. J. (2002). Integrating mRNA processing with transcription. Cell 108(4), 501-512.
147. Pugh, B. F. (2000). Control of gene expression through regulation of the TATA-binding protein. Gene 255(1), 1-14.
148. Raschke, E. E., Albert, T., and Eick, D. (1999). Transcriptional regulation of the Ig kappa gene by promoter-proximal pausing of RNA polymerase II. J. Immunol. 168(8), 4375-4382.
149. Rudd, M. D., Izban, M. G., and Luse, D. S. (1994). The active site of RNA polymerase II participates in transcript cleavage within arrested ternary complexes. Proc. Natl. Acad. Sci. USA 91, 8057-8061.
150. Sadhale, P. P., and Woychik, N. A. (1994). C25, an essential RNA polymerase III subunit related to the RNA polymerase II subunit RPB7. Mol. Cell. Biol. 14(9), 6164-6170.
151. Sakurai, H., Mitsuzawa, H., Kimura, M., and Ishihama, A. (1999). The Rpb4 subunit of fission yeast Schizosaccharomyces pombe RNA polymerase II is essential for cell viability and similar in structure to the corresponding subunits of higher eukaryotes. Mol. Cell. Biol. 19(11), 7511-7518.
152. Samkurashvili, I., and Luse, D. S. (1996). Translocation and transcriptional arrest during transcript elongation by RNA polymerase II. J. Biol. Chem. 271(38), 23495-23505.
153. Samkurashvili, I., and Luse, D. S. (1998). Structural changes in the RNA polymerase II transcription complex during transition from initiation to elongation. Mol. Cell. Biol. 18(9), 5343-5354.
154. Sawaya, M. R., Prasad, R., Wilson, S. H., Kraut, J., and Pelletier, H. (1997). Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism. Biochemistry 36(37), 11205-11215.
155. Shatkin, A. J., and Manley, J. L. (2000). The ends of the affair: capping and polyadenylation. Nat. Struct. Biol. 7(10), 838-842.
156. Shaw, P. E. (2002). Peptidyl-prolyl isomerases: a new twist to transcription. EMBO Rep. 3(6), 521-526.
157. Sheffer, A., Varon, M., and Choder, M. (1999). Mol. Cell. Biol. 19, 2672-2680.
158. Shilatifard, A. (1998a). Factors regulating the transcriptional elongation activity of RNA polymerase II. FASEB J. 12, 1437-1446.
159. Shilatifard, A. (1998b). The RNA polymerase II general elongation complex. Biol. Chem. 379(1), 27-31.
160. Shpakovski, G. V., and Shematorova, E. K. (1999). Characterization of the rpa43+ cDNA of Schizosacharomyces pombe: structural similarity of subunit Rpa43 of RNA polymerase I and subunit Rpe25 of RNA polymerase III. Russ. J. Bioorgan. Chem. 25(10), 700-704.
161. Siaut, M., Zaros, C., Levivier, E., Ferri, M. L., Court, M., Werner, M., Callebaut, I., Thuriaux, P., Sentenac, A., and Conesa, C. (2003). An Rpb4/Rpb7-like complex in yeast RNA polymerase III contains the orthologue of mammalian CGRP-RCP. Mol. Cell. Biol. 23(1), 195-205.
162. Sidorenkov, I., Komissarova, N., and Kashlev, M. (1998). Crucial role of the RNA:DNA hybrid in the processivity of transcription. Mol. Cell 2, 55-64.
163. Smale, S. T., Jain, A., Kaufmann, J., Emami, K. H., Lo, K., and Garraway, I. P. (1998). The initiator element: a paradigm for core promoter heterogeneity within metazoan protein-coding genes. Cold Spring Harb. Symp. Quant. Biol. 63, 21-31.
164. Sosunov, V., Sosunova, E., Mustaev, A., Bass, I., Nikiforov, V., and Goldfarb, A. (2003). Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase. EMBO J. 22, 2234-2244.
165. Steinmetz, E. J. (1997). Pre-mRNA processing and the CTD of RNA polymerase II: the tail that wags the dog? Cell 89(4), 491-494.
166. Steitz, T. A. (1999). DNA polymerases: structural diversity and common mechanisms. J. Biol. Chem. 274(25), 17395-17398.
167. Strasser, K., Masuda, S., Mason, P., Pfannstiel, J., Oppizzi, M., Rodriguez-Navarro, S., Rondon, A. G., Aguilera, A., Struhl, K., Reed, R., and Hurt, E. (2002). TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417(6886), 304-308.
168. Sweetser, D., Nonet, M., and Young, R. A. (1987). Prokaryotic and eukaryotic RNA polymerases have homologous core subunits. Proc. Natl. Acad. Sci. USA 84, 1192-1196.
169. Szentirmay, M. N., and Sawadogo, M. (2000). Spatial organization of RNA polymerase II transcription in the nucleus. Nucleic Acids Res. 28(10), 2019-2025.
170. Tahirov, T. H., Temiakov, D., Anikin, M., Patlan, V., McAllister, W. T., Vassylyev, D. G., and Yokoyama, S. (2002). Structure of a T7 RNA polymerase elongation complex at 2.9 resolution. Nature 420(6911), 43-50.
171. Tan, Q., Linask, K. L., Ebright, R. H., and Woychik, N. A. (2000a). Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria. Genes Dev. 14(3), 339-348.
172. Tan, Q., Linask, K. L., Ebright, R. H., and Woychik, N. A. (2000b). Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria. Genes Dev. 14(3), 339-348.
173. Thomas, M. J., Platas, A. A., and Hawley, D. K. (1998). Transcriptional fidelity and proofreading by RNA polymerase II. Cell 93(4), 627-637.
174. Thuillier, V., Brun, I., Sentenac, A., and Werner, M. (1996). Mutations in the alpha amanitin conserved domain of the largest subunit of yeast RNA polymerase III affect pausing, RNA cleavage and transcriptional transitions. EMBO J. 15, 618-629.
175. Todone, F., Brick, P., Werner, F., Weinzierl, R. O., and Onesti, S. (2001). Structure of an archaeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex. Mol. Cell 8(5), 1137-1143.
176. Todone, F., Weinzierl, R. O., Brick, P., and Onesti, S. (2000). Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target. Proc. Natl. Acad. Sci. USA 97(12), 6306-6310.
177. Toulokhonov, I., Artsimovitch, I., and Landick, R. (2001). Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science 292(5517), 730-733.
178. Tsai, F. T., and Sigler, P. B. (2000). Structural basis of preinitiation complex assembly on human pol II promoters. EMBO J. 19(1), 25-36.
179. Ujvari, A., Pal, M., and Luse, D. S. (2002). RNA polymerase II transcription complexes may become arrested if the nascent RNA is shortened to less than 50 nucleotides. J. Biol. Chem. 277(36), 32527-32537.
180. Uptain, S. M., Kane, C. M., and Chamberlin, M. J. (1997). Basic mechanisms of transcript elongation and its regulation. Annu. Rev. Biochem. 66, 117-172.
181. 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 (6890), 712-719.
182. von Hippel, P. H. (1998). An integrated model of the transcription complex in elongation, termination, and editing. Science 281, 660-665.
183. Wang, B., Jones, D. N., Kaine, B. P., and Weiss, M. A. (1998). High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases. Structure 6(5), 555-569.
184. Wang, D., and Hawley, D. K. (1993). Identification of a 3′-5′ exonucldase activity associated with human RNA polymerase II. Proc. Natl. Acad. Sci. USA 90, 843-847.
185. Wang, W., Carey, M., and Gralla, J. D. (1992). Polymerase II promoter activation: closed complex formation and ATP-driven start site opening. Science 255, 450-452.
186. Wang, X., Spangler, L., and Dvir, A. (2003). Promoter escape by RNA polymerase II: downstream promoter DNA is required during multiple steps of early transcription. J. Biol. Chem. 278, 10250-10256.
187. Weilbaecher, R. G., Awrey, D. E., Edwards, A. M., and Kane, C. M. (2003). Intrinsic transcript cleavage in yeast RNA polymerase II elongation complexes. J. Biol. Chem. 278, 24189-24199.
188. Werner, F., Eloranta, J. J., and Weinzierl, R. O. (2000). Archaeal RNA polymerase subunits F and P are bona fide homologs of eukaryotic RPB4 and RPB12. Nucleic Acids Res. 28(21), 4299-4305.
189. West, M. L., and Corden, J. L. (1995). Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations. Genetics 140(4), 1223-1233.
190. Wooddell, C. I., and Burgess, R. R. (2000). Topology of yeast RNA polymerase II subunits in transcription elongation complexes studied by photoaffinity cross-linking [in process citation]. Biochemistry 39(44), 13405-13421.
191. Woychik, N. A. (1998). Fractions to functions: RNA polymerase II thirty years later. Cold Spring Harb. Symp. Quant. Biol. 63, 311-317.
192. Woychik, N. A., and Young, R. A. (1989). RNA polymerase II subunit RPB4 is essential for high- and low-temperature yeast cell growth. Mol. Cell. Biol. 9, 2854-2859.
193. Yankulov, K., Blau, J., Purton, T., Roberts, S., and Bentley, D. L. (1994). Transcriptional elongation by RNA polymerase II is stimulated by transactivators. Cell 77 (5), 749-759.
194. Yin, Y. W., and Steitz, T. A. (2002). Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science 298(5597), 1387-1395.
195. Yuan, X., Zhao, J., Zentgraf, H., Hoffmann-Rohrer, U., and Grummt, I. (2002). Multiple interactions between RNA polymerase I, TIF-1A and TAFI subunits regulate preinitiation complex assembly at the ribosomal gene promoter. EMBO Rep. 3(11), 1082-1087.
196. Yudkovsky, N., Ranish, J. A., and Hahn, S. (2000). A transcription reinitiation intermediate that is stabilized by activator. Nature 408 (6809), 225-229.
197. Zaychikov, E., Martin, E., Denissova, L., Kozlov, M., Markovtsov, V., Kashlev, M., Heumann, H., Nikiforov, V., Goldfarb, A., and Mustaev, A. (1996). Mapping of catalytic residues in the RNA polymerase active center. Science 273, 107-109.
198. 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 [see comments]. Cell 98(6), 811-824.
199. Zhang, G., and Darst, S. A. (1998). Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain. Science 281 (5374), 262-266.
200. Zhang, J., and Corden, J. L. (1991). Phosphorylation causes a conformational change in the carboxyl-terminal domain of the mouse RNA polymerase II largest subunit. J. Biol. Chem. 266, 2297-2302.