The RNA polymerase II core promoter: A key component in the regulation of gene expression

Genes and Development

Volumn 16, Issue 20, 2002, Pages 2583-2592

  Butler, Jennifer E F ^a   Kadonaga, James T ^b  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^b SECTION OF MOLECULAR BIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE II;

CPG ISLAND; GENE CONTROL; GENE EXPRESSION REGULATION; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; TATA BOX; TRANSCRIPTION REGULATION;

ANIMALS; ENHANCER ELEMENTS (GENETICS); GENE EXPRESSION REGULATION; HUMANS; PROMOTER REGIONS (GENETICS); RNA POLYMERASE II; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 0037108159     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.1026202     Document Type: Review

References (120)

1. Adachi, N. and Lieber, M.R. 2002. Bidirectional gene organization: A common architectural feature of the human genome. Cell 109: 807-809.
2. Albright, S.R. and Tjian, R. 2000. TAFs revisited: More data reveal new twists and confirm old ideas. Gene 242: 1-13.
3. Antequera, F. and Bird, A. 1993. Number of CpG islands and genes in human and mouse. Proc. Natl. Acad. Sci. 90: 11995-11999.
4. II60. Mol. Cell. Biol. 21: 6808-6819.
5. Arkhipova, I.R. 1995. Promoter elements in Drosophila melanogaster revealed by sequence analysis. Genetics 139: 1359-1369.
6. Benson, L.Q., Coon, M.R., Krueger, L.M., Han, G.C., Sarnaik, A.A., and Wechsler, D.S. 1999. Expression of MXI1, a Myc antagonist, is regulated by Sp1 and AP2. J. Biol. Chem. 274: 28794-28802.
7. Berk, A.J. 2000. TBP-like factors come into focus. Cell. 103: 5-8.
8. Bird, A.P. 1986. CpG-rich islands and the function of DNA methylation. Nature 321: 209-213.
9. Bird, A.P. 1993. Functions for DNA methylation in vertebrates. Cold Spring Harb. Symp. Quant. Biol. 58: 281-285.
10. Blackwood, E.M. and Kadonaga, J.T. 1998. Going the distance: A current view of enhancer action. Science 281: 60-63.
11. Brandeis, M., Frank, D., Keshet, I., Siegfried, Z., Mendelsohn, M., Nemes, A., Temper, V., Razin, A., and Cedar, H. 1994. Sp1 elements protect a CpG island from de novo methylation. Nature 371: 435-438.
12. Breathnach, R. and Chambon, P. 1981. Organization and expression of eucaryotic split genes coding for proteins. Annu. Rev. Biochem. 50: 349-383.
13. Bucher, P. 1990. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212: 563-578.
14. Bulger, M. and Groudine, M. 1999. Looping versus linking: Toward a model for long-distance gene activation. Genes & Dev. 13: 2465-2477.
15. 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.
16. II60 of Drosophila. Genes & Dev. 11: 3020-3031.
17. Burke, T.W., Willy, P.J., Kutach, A.K., Butler, J.E.F., 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.
18. Burley, S.K. and Roeder, R.G. 1996. Biochemistry and structural biology of transcription factor IID (TFIID). Annu. Rev. Biochem. 65: 769-799.
19. Butler, J.E.F. and Kadonaga, J.T. 2001. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes & Dev. 15: 2515-2519.
20. Carcamo, J., Buckbinder, L., and Reinberg, D. 1991. The initiator directs the assembly of a transcription factor IID-dependent transcription complex. Proc. Natl. Acad. Sci. 88: 8052-8056.
21. II150 complex recognizes the initiator. EMBO J. 18: 4835-4845.
22. Cheriyath, V., Novina, C.D., and Roy, A.L. 1998. TFII-I regulates Vβ promoter activity through an initiator element. Mol. Cell. Biol. 18: 4444-4454.
23. Collart, M.A. and Struhl, K. 1994. NOT1 (CDC39), NOT2 (CDC36), NOT3, and NOT4 encode a global-negative regulator of transcription that differentially affects TATA-element utilization. Genes & Dev. 8: 525-537.
24. Corden, J., Wasylyk, B., Buchwalder, A., Sassone-Corsi, P., Kedinger, C., and Chambon, P. 1980. Promoter sequences of eukaryotic protein-coding genes. Science 209: 1406-1414.
25. Courey, A.J. and Jia, S. 2001. Transcriptional repression: The long and the short of it. Genes & Dev. 15: 2786-2796.
26. Crowley, T.E., Hoey, T., Liu, J.-K., Jan, Y.N., Jan, L.Y., and Tjian, R. 1993. A new factor related to TATA-binding protein has highly restricted expression patterns in Drosophila. Nature. 361: 557-561.
27. Dantonel, J.-C., Quintin, S., Lakatos, L., Labouesse, M., and Tora, L. 2000. TBP-like factor is required for embryonic RNA polymerase II transcription in C. elegans. Mol. Cell 6: 715-722.
28. Dvir, A., Conaway, J.W., and Conaway, R.C. 2001. Mechanism of transcription initiation and promoter escape by RNA polymerase II. Curr. Opin. Genet. Dev. 11: 209-214.
29. Emami, K.H., Navarre, W.W., and Smale, S.T. 1995. Core promoter specificities of the Sp1 and VP16 transcriptional activation domains. Mol. Cell. Biol. 15: 5906-5916.
30. Emerson, B. 2002. Specificity of gene regulation. Cell 109: 267- 270.
31. Evans, R., Fairley, J.A., and Roberts, S.G.E. 2001. Activator-mediated disruption of sequence-specific DNA contacts by the general transcription factor TFIIB. Genes & Dev. 15: 2945-2949.
32. Gardiner-Garden, M. and Frommer, M. 1987. CpG islands in vertebrate genomes. J. Mol. Biol. 196: 261-282.
33. Garraway, I.P., Semple, K., and Smale, S.T. 1996. Transcription of the lymphocyte-specific terminal deoxynucleotidyltransferase gene requires a specific core promoter structure. Proc. Natl. Acad. Sci. 93: 4336-4341.
34. Glass, C.K., and Rosenfeld, M.G. 2000. The coregulator exchange in transcriptional functions of nuclear receptors. Genes & Dev. 14: 121-141.
35. Goldberg, M.L. 1979. "Sequence analysis of Drosophila histone genes." Ph.D. dissertation, Stanford University, California.
36. Grueneberg, D.A., Henry, R.W., Brauer, A., Novina, C.D., Cheriyath, V., Roy, A.L., and Gilman, M. 1997. A multifunctional DNA-binding protein that promotes the formation of serum response factor/homeodomain complexes: Identity to TFII-I. Genes & Dev. 11: 2482-2493.
37. Hampsey, M. 1998. Molecular genetics of the RNA polymerase II general transcription machinery. Microbiol. Mol. Biol. Rev. 62: 465-503.
38. Hansen, S.K., Takada, S., Jacobson, R.H., Lis, J.T., and Tjian, R. 1997. Transcription properties of a cell type-specific TATA- binding protein, TRF. Cell 91: 71-83.
39. Holmes, M.C. and Tjian, R. 2000. Promoter-selective properties of the TBP-related factor TRF1. Science 288: 867-870.
40. Hultmark, D., Klemenz, R., and Gehring, W.J. 1986. Translational and transcriptional control elements in the untranslated leader of the heat-shock gene hsp22. Cell 44: 429-438.
41. Ince, T.A. and Scotto, K.W. 1995. A conserved downstream element defines a new class of RNA polymerase II promoters. J. Biol. Chem. 270: 30249-30252.
42. C TATA elements. Mol. Cell. Biol. 15: 7059-7066.
43. Javahery, R., Khachi, A., Lo, K., Zenzie-Gregory, B., and Smale, S.T. 1994. DNA sequence requirements for transcriptional initiator activity in mammalian cells. Mol. Cell. Biol. 14: 116-127.
44. Kaltenbach, L., Horner, M.A., Rothman, J.H. and Mango, S.E. 2000. The TBP-like factor CeTLF is required to activate RNA polymerase II transcription during C. elegans embryogenesis. Mol. Cell 6: 705-713.
45. Kaufmann, J. and Smale, S.T. 1994. Direct recognition of initiator elements by a component of the transcription factor IID complex. Genes & Dev. 8: 821-829.
46. Kaufmann, J., Ahrens, K., Koop, R., Smale, S.T., and Müller, R. 1998. CIF150, a human cofactor for transcription factor IID-dependent initiator function. Mol. Cell. Biol. 18: 233-239.
47. Kuras, L., Kosa, P., Mencia, M., and Struhl, K. 2000. TAF-containing and TAF-independent forms of transcriptionally active TBP in vivo. Science 288: 1244-1248.
48. Kutach, A.K. and Kadonaga, J.T. 2000. The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol. Cell. Biol. 20: 4754-4764.
49. 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: 34-44.
50. Lee, T.I., and Young, R.A. 2000. Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet. 34: 77-137.
51. Lefstin, J.A. and Yamamoto, K.R. 1998. Allosteric effects of DNA on transcriptional regulators. Nature 392: 885-888.
52. Lemon, B. and Tjian, R. 2000. Orchestrated response: A symphony of transcription factors for gene control. Genes & Dev. 14: 2551-2569.
53. Lewis, B.A., Kim, T.-K. and Orkin, S.H. 2000. A downstream element in the human β-globin promoter: Evidence of extended sequence-specific transcription factor IID contacts. Proc. Natl. Acad. Sci. 97: 7172-7177.
54. Li, X. and Noll, M. 1994. Compatibility between enhancers and promoters determines the transcriptional specificity of gooseberry and gooseberry neuro in the Drosophila embryo. EMBO J. 13: 400-406.
55. Li, X.-Y., Bhaumik, S.R., and Green, M.R. 2000. Distinct classes of yeast promoters revealed by differential TAF recruitment. Science 288: 1242-1244.
56. Li, X.-Y., Bhaumik, S.R., Zhu, X., Li, L., Shen, W.-C., Dixit, B.L. and Green, M.R. 2002. Selective recruitment of TAFs by yeast upstream activating sequences: Implications for eukaryotic promoter structure. Curr. Biol. 12: 1240-1244.
57. Lo, K. and Smale, S.T. 1996. Generality of a functional initiator consensus sequence. Gene 182: 13-22.
58. Luo, Y. and Roeder, R.G. 1995. Cloning, functional characterization, and mechanism of action of the B-cell-specific transcriptional coactivator OCA-B. Mol. Cell. Biol. 15: 4115- 4124.
59. Luo, Y., Fujii, H., Gerster, T., and Roeder, R.G. 1992. A novel B cell-derived coactivator potentiates the activation of immunoglobulin promoters by octamer-binding transcription factors. Cell 71: 231-241.
60. Macleod, D., Charlton, J., Mullins, J., and Bird, A.P. 1994. Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Genes & Dev. 8: 2282-2292.
61. C, an unusual promoter element required for constitutive transcription of the yeast HIS3 gene. Mol. Cell. Biol. 10: 4447-4455.
62. Maldonado, E. 1999. Transcriptional functions of a new mammalian TATA-binding protein-related factor. J. Biol. Chem. 274: 12963-12966.
63. Maldonado, E., Hampsey, M., and Reinberg, D. 1999. Repression: Targeting the heart of the matter. Cell 99: 455-458.
64. Martinez, E., Chiang, C.-M., Ge, H., and Roeder, R.G. 1994. TATA-binding protein-associated factor(s) in TFIID function through the initiator to direct basal transcription from a TATA-less class II promoter. EMBO J. 13: 3115-3126.
65. II150- containing TFIID complex. Mol. Cell. Biol. 18: 6571-6583.
66. McKenna, N.J. and O'Malley, B.W. 2002. Combinatorial control of gene expression by nuclear receptors and coregulators. Cell 108: 465-474.
67. Mencía, M., Moqtaderi, Z., Geisberg, J.V., Kuras, L., and Struhl, K. 2002. Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast. Mol. Cell 9: 823-833.
68. Merli, C., Bergstrom, D.E., Cygan, J.A., and Blackman, R.K. 1996. Promoter specificity mediates the independent regulation of neighboring genes. Genes & Dev. 10: 1260-1270.
69. Moore, P.A., Ozer, J., Salunek, M., Jan, G., Zerby, D., Campbell, S., and Lieberman, P.M. 1999. A human TATA binding protein-related protein with altered DNA binding specificity inhibits transcription from multiple promoters and activators. Mol. Cell. Biol. 19: 7610-7620.
70. 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.
71. Moqtaderi, Z., Keaveney, M., and Struhl, K. 1998. The histone H3-like TAF is broadly required for transcription in yeast. Mol. Cell 2: 675-682.
72. Myer, V.E. and Young, R.A. 1998. RNA polymerase II holoenzymes and subcomplexes. J. Biol. Chem. 273: 27757-27760.
73. Nakatani, Y., Brenner, M., and Freese, E. 1990a. An RNA polymerase II promoter containing sequences upstream and downstream from the RNA startpoint that direct initiation of transcription from the same site. Proc. Natl. Acad. Sci. 87: 4289-4293.
74. Nakatani, Y., Horikoshi, M., Brenner, M., Yamamoto, T., Besnard, F., Roeder, R.G., and Freese, E. 1990b. A downstream initiation element required for efficient TATA box binding and in vitro function of TFIID. Nature 348: 86-88.
75. Narlikar, G.J., Fan, H.-Y., and Kingston, R.E. 2002. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108: 475-487.
76. Oelgeschläger, T., Chiang, C.-M., and Roeder, R.G. 1996. Topology and reorganization of a human TFIID-promoter complex. Nature 382: 735-738.
77. Ohbayashi, T., Makino, Y., and Tamura, T. 1999. Identification of a mouse TBP-like protein (TLP) distantly related to the Drosophila TBP-related factor. Nucleic Acids Res. 27: 750-755.
78. Ohtsuki, S., Levine, M., and Cai, H.N. 1998. Different core promoters possess distinct regulatory activities in the Drosophila embryo. Genes & Dev. 12: 547-556.
79. Orphanides, G., Lagrange, T. and Reinberg, D. 1996. The general transcription factors of RNA polymerase II. Genes & Dev. 10: 2657-2683.
80. Orphanides, G. and Reinberg, D. 2002. A unified theory of gene expression. Cell 108: 439-451.
81. Pribnow, D. 1975a. Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Proc. Natl. Acad. Sci. 72: 784-788.
82. Pribnow, D. 1975b. Bacteriophage T7 early promoters: Nucleotide sequences of two RNA polymerase binding sites. J. Mol. Biol. 99: 419-443.
83. Purnell, B.A., Emanuel, P.A., and Gilmour, D.S. 1994. TFIID sequence recognition of the initiator and sequences farther downstream in Drosophila class II genes. Genes & Dev. 8: 830-842.
84. Qureshi, S.A. and Jackson, S.P. 1998. Sequence-specific DNA binding by the S. shibatae TFIIB homolog, TFB, and its effect on promoter strength. Mol. Cell 1: 389-400.
85. Rabenstein, M.D., Zhou, S., Lis, J.T., and Tjian, R. 1999. TATA box-binding protein (TBP)-related factor 2 (TRF2), a third member of the TBP family. Proc. Natl. Acad. Sci. 96: 4791-4796.
86. Roeder, R.G. 1998. Role of general and gene-specific cofactors in the regulation of eukaryotic transcription. Cold Spring Harb. Symp. Quant. Biol. 58: 201-218.
87. Roy, A.L., Du, H., Gregor, P.D., Novina, C.D., Martinez, E., and Roeder, R.G. 1997. Cloning of an Inr- and E-box-binding protein, TFII-I, that interacts physically and functionally with USF1. EMBO J. 16: 7091-7104.
88. Roy, A.L., Meisterernst, M., Pognonec, P., and Roeder, R.G. 1991. Cooperative interaction of an initiator-binding transcription initiation factor and the helix-loop-helix activator USF. Nature 354: 245-248.
89. Rudge, T.L. and Johnson, L.F. 1999. Inactivation of MED-1 elements in the TATA-less, initiator-less mouse thymidylate synthase promoter has no effect on promoter strength or the complex pattern of transcriptional start sites. J. Cell. Biochem. 73: 90-96.
90. Simon, M.C., Fisch, T.M., Benecke, B.J., Nevins, J.R., and Heintz, N. 1988. Definition of multiple, functionally distinct TATA elements, one of which is a target in the hsp70 promoter for E1A recognition. Cell 52: 723-729.
91. Singer, V.L., Wobbe, C.R., and Struhl, K. 1990. A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation. Genes & Dev. 4: 636-645.
92. Smale, S.T. 1994. Core promoter architecture for eukaryotic protein-coding genes. In Transcription: Mechanisms and regulation (eds R.C. Conaway and J.W. Conaway), pp. 63-81. Raven Press, Ltd., New York.
93. Smale, S.T. 1997. Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes. Biochim. Biophys. Acta 1351: 73-88.
94. Smale, S.T. 2001. Core promoters: Active contributors to combinatorial gene regulation. Genes & Dev. 15: 2503-2508.
95. Smale, S.T. and Baltimore, D. 1989. The "initiator" as a transcription control element. Cell 57: 103-113.
96. 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. 58: 21-31.
97. Smale, S.T., Schmidt, M.C., Berk, A.J., and Baltimore, D. 1990. Transcriptional activation by Sp1 as directed through TATA or initiator: Specific requirement for mammalian transcription factor IID. Proc. Natl. Acad. Sci. 87: 4509-4513.
98. II40 protein is encoded by the e(y)1 gene: Biological consequences of mutations. Mol. Cell. Biol. 19: 3769-3778.
99. Strahl, B.D. and Allis, C.D. 2000. The language of covalent histone modifications. Nature 403: 41-45.
100. Struhl, K. 1986. Constitutive and inducible Saccharomyces cerevisiae promoters: Evidence for two distinct molecular mechanisms. Mol. Cell. Biol. 6: 3847-3853.
101. Struhl, K. 1987. Promoters, activator proteins, and the mechanism of transcriptional initiation in yeast. Cell 49: 295-297.
102. Struhl, K. 1999. Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98: 1-4.
103. Suzuki, Y., Tsunoda, T., Sese, J., Taira, H., Mizushima-Sugano, J., Hata, H., Ota, T., Isogai, T., Tanaka, T., Nakamura, Y., et al. 2001. Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Genome Res. 11: 677-684.
104. Takada, S., Lis, J.T., Zhou, S., and Tjian, R. 2000. A TRF1:BRF complex directs Drosophila RNA polymerase III transcription. Cell 101: 459-469.
105. Teichmann, M., Wang, Z., Martinez, E., Tjernberg, A., Zhang, D., Vollmer, F., Chait, B.T., and Roeder, R.G. 1999. Human TATA-binding protein-related factor-2 (hTRF2) stably associates with hTFIIA in HeLa cells. Proc. Natl. Acad. Sci. 96: 13720-13725.
106. Tora, L. 2002. A unified nomenclature for TATA box binding protein (TBP)-associated factors (TAFs) involved in RNA polymerase II transcription. Genes & Dev. 16: 673-675.
107. Tsai, F.T.F. and Sigler, P.B. 2000. Structural basis of preinitiation complex assembly on human Pol II promoters. EMBO J. 19: 25-36.
108. Usheva, A. and Shenk, T. 1994. TATA-binding protein-independent initiation: YY1, TFIIB, and RNA polymerase II direct basal transcription on supercoiled template DNA. Cell 76: 1115-1121.
109. Verrijzer, C.P. 2001. Transcription factor IID-Not so basal after all. Science 293: 2010-2011.
110. II150: Similarity to yeast gene TSM-1 and specific binding to core promoter DNA. Science 264: 933-941.
111. 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.
112. Wefald, F.C., Devlin, B.H., and Williams, R.S. 1990. Functional heterogeneity of mammalian TATA-box sequences revealed by interaction with a cell-specific enhancer. Nature 344: 260-262.
113. Weis, L., and Reinberg, D. 1992. Transcription by RNA polymerase II: Initiator-directed formation of transcription-competent complexes. FASEB J. 6: 3300-3309.
114. Weis, L. and Reinberg, D. 1997. Accurate positioning of RNA polymerase II on a natural TATA-less promoter is independent of TATA-binding-protein-associated factors and initiator-binding proteins. Mol. Cell. Biol. 17: 2973-2984.
115. West, A.G., Gaszner, M., and Felsenfeld, G. 2002. Insulators: Many functions, many mechanisms. Genes & Dev. 16: 271-288.
116. White, R.J. 2001. Gene transcription: Mechanisms and control, Blackwell Science, Oxford, UK.
117. Willy, P.J., Kobayashi, R., and Kadonaga, J.T. 2000. A basal transcription factor that activates or represses transcription. Science 290: 982-984.
118. Woychik, N.A. and Hampsey, M. 2002. The RNA polymerase II machinery: Structure illuminates function. Cell 108: 453-463.
119. Zhang, Y. and Reinberg, D. 2001. Transcription regulation by histone methylation: Interplay between different covalent modifications of the core histone tails. Genes & Dev. 15: 2343-2360.
120. II55 gene contains a functional initiator and a downstream promoter element. J. Biol. Chem. 276: 25503-25511.