DNA binding site selection by RNA polymerase II TAFs: A TAF(II)250-TAF(II)150 complex recognizes the initiator

EMBO Journal

Volumn 18, Issue 17, 1999, Pages 4835-4845

  Chalkley, Gillian E ^a,b   Verrijzer, C Peter ^a,b  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^b LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Core promoter; Initiator; TAFs; TFIID; Transcription

Indexed keywords

BINDING PROTEIN; RNA POLYMERASE II; TATA BINDING PROTEIN; TATA BINDING PROTEIN ASSOCIATED FACTOR; TRANSCRIPTION FACTOR SP1; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BINDING SITE; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA BINDING; DNA SEQUENCE; DNA STRUCTURE; GENETIC TRANSCRIPTION; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; PROMOTER REGION; TATA BOX; TRANSCRIPTION INITIATION;

AMINO ACID SEQUENCE; BASE SEQUENCE; BINDING SITES; DNA-BINDING PROTEINS; HUMANS; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEAR PROTEINS; PROMOTER REGIONS (GENETICS); RECOMBINANT PROTEINS; RNA POLYMERASE II; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; TATA-BINDING PROTEIN ASSOCIATED FACTORS; TRANS-ACTIVATION (GENETICS); TRANSCRIPTION FACTOR TFIID; TRANSCRIPTION FACTORS; TRANSCRIPTION FACTORS, TFII; TRANSCRIPTION, GENETIC;

EID: 0033200098     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/18.17.4835     Document Type: Article

References (68)

1. Aravind, L. and Landsman, D. (1998) AT-hook motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res., 26, 4413-4421.
2. Arkhipova, I.R. (1995) Promoter elements in Drosophila melanogaster revealed by sequence analysis. Genetics, 139, 1359-1369.
3. Aso, T., Conaway, J.W. and Conaway, R.C. (1994) Role of core promoter structure in assembly of the RNA polymerase II preinitiation complex. A common pathway for formation of preinitiation intermediates at many TATA and TATA-less promoters. J. Biol. Chem., 269, 26575-26583.
4. Auble, D.T., Hansen, K.E., Mueller, C.G., Lane, W.S., Thorner, J. and Hahn, S. (1994) Mot1, a global repressor of RNA polymerase II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism. Genes Dev., 8, 1920-1934.
5. Austin, R.J. and Biggin, M.D. (1996) Purification of the Drosophila RNA polymerase II general transcription factors. Proc. Natl Acad. Sci. USA, 12, 5788-5792.
6. Bianchi, M.E. (1988) Interaction of a protein from rat liver nuclei with cruciform DNA. EMBO J., 7, 843-849.
7. Burke, T.W. and Kadanoga, J.T. (1996) Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. Genes Dev., 10, 711-724.
8. II60 of Drosophila. Genes Dev., 11, 3020-3031.
9. Burley, S.K. and Roeder, R.G. (1996) Biochemistry and structural biology of transcription factor IID (TFIID). Annu. Rev. Biochem., 65, 769-799.
10. Burley, S.K. and Roeder, R.G. (1998) TATA box mimicry by TFIID: autoinhibition of Pol II transcription. Cell, 94, 551-553.
11. 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. USA., 88, 8052-8056.
12. Chen, J.-L. and Tjian, R. (1996) Reconstitution of TATA-binding protein associated factor/TATA-binding protein complexes for in vitro transcription. Methods Enymol., 273, 208-217.
13. Chen, J.-L., 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.
14. Chi, T. and Carey, M. (1996) Assembly of the isomerized TFIIA-TFIID-TATA ternary complex is necessary and sufficient for gene activation. Genes Dev., 10, 2540-2550.
15. Das, G., Hinkley, C.S. and Herr, W. (1995) Basal promoter elements as selective determinants of transcriptional activator function. Nature, 374, 657-660.
16. Emami, K.H., Navarre, W. and Smale, S.T. (1995) Core promoter specificities of the Sp1 and VP16 transcription activation domains. Mol. Cell. Biol., 15, 5906-5916.
17. Emami, K.H., Jain, A. and Smale, S.T. (1997) Mechanism of synergy between TATA and initiator: synergistic binding of TFIID following a putative TFIIA-induced isomerization. Genes Dev., 11, 3007-3019.
18. Emanuel, P.A. and Gilmour, D.S. (1993) Transcription factor TFIID recognizes DNA sequences downstream of the TATA element in the hsp70 heat shock gene. Proc. Natl Acad. Sci. USA, 90, 8449-8453.
19. Gilmour, D.S., Dietz, T.J. and Elgin, S.C. (1990) UV cross-linking identifies four polypeptides that require the TATA box to bind to the Drosophila hsp 70 promoter. Mol. Cell. Biol., 10, 4233-4238.
20. Hahn, S. (1998) The role of TAFs in RNA polymerase II transcription. Cell, 95, 579-582.
21. Hampsey, M. (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. Mol. Rev., 62, 465-503.
22. Hampsey, M. and Reinberg, D. (1997) Transcription: why are TAFs essential? Curr. Biol., 7, R44-R46.
23. Hansen, S. and Tjian, R. (1995) TAFs and TFIIA mediate differential utilization of the tandem Adh promoters. Cell, 82, 565-575.
24. 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
25. Harlow, E. and Lane, D. (1988) Antibodies: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
26. Hernandez, N. (1993) TBP, a universal eukaryotic transcription factor? Genes Dev., 7, 1291-1308.
27. Hoffmann, A., Oelgeschläger, 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.
28. Horikoshi, M., Hai, T., Lin, Y.S., Green, M.R. and Roeder, R.G. (1988) Transcription factor ATF interacts with the TATA factors to facilitate establishment of a pre-initiation complex. Cell, 54, 1033-1042.
29. II30 is present in a distinct TFIID complex and is required for transcriptional activation by the estrogen receptor. Cell, 79, 107-117.
30. Kadonaga, J.T. (1990) Assembly and disassembly of the Drosophilia RNA polymerase II complex during transcription. J. Biol. Chem., 265, 2624-2631.
31. Kaufmann, J., and Smale, S. (1994) Direct recognition of initiator elements by a component of the transcription factor IID complex. Genes Dev., 8, 821-829.
32. Kaufmann, J., Verrijzer, C.P., Shao, J. and Smale, S.T. (1996) CIF, an essential cofactor for TFIID-dependent initiator function. Genes Dev., 10, 873-886.
33. Kaufmann, J., Ahrens, K., Koop, R., Smale, S.T. and Müller, R. (1998) CIF150, a human cofactor for TFIID-dependent initiator function. Mol. Cell. Biol., 18, 233-239.
34. Kokubo, T., Gong, D.-W., Yasmashita, S., Horikoshi, M., Roeder, R.G. and Nakatani, Y. (1993) Drosophila 230-kD TFIID subunit, a functional homolog of the human cell cycle product, negatively regulates DNA binding of the TATA box-binding subunit of TFIID. Genes Dev., 7. 1033-1046.
35. 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.
36. Lee, T.I. and Young, R.A. (1998) Regulation of gene expression by TBP-associated proteins. Genes Dev., 12, 1398-1408.
37. Lefstin, J.A. and Yamamoto, K.R. (1998) Allosteric effects of DNA on transcriptional regulators. Nature, 392, 585-588.
38. II230 complex: protein mimicry of the minor groove surface of the TATA box unwound by TBP. Cell, 94, 573-583.
39. Martinez, E., Chiang, C.-M., Ge, H. and Roeder, R.G. (1994) TAFs in TFIID function through the initiator to direct basal transcription from a TATA-less class II promoter. EMBO J., 13, 3115-3126.
40. Martinez, E., Zhou, Q., L'Etoille, N.D., Oelgeschläger, T., Berk, A.J. and Roeder, R.G. (1995) Core promoter-specific function of a mutant transcription factor TFIID defective in TATA-box binding. Proc. Natl Acad. Sci. USA, 92, 11864-11868.
41. II150-containing TFIID complex. Mol. Cell. Biol., 18, 6571-6583.
42. Nakatani, Y., Horikoshi, M., Brenner, M., Yamamoto, T., Bresnard, F., Roeder, R.G. and Freese, E. (1990) A downstream initiation element required for efficient TATA box-binding and in vitro function of TFIID. Nature, 348, 86-88.
43. Oelgeschläger, T., Chiang, C.-M. and Roeder, R.G. (1996) Topology and reorganization of a human TFIID-promoter complex. Nature, 382, 735-738.
44. 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.
45. Orphanides, G., Lagrange, T. and Reinberg, D. (1996) The general transcription factors of RNA polymerase II. Genes Dev., 10, 2657-2683.
46. Pollock, R. and Treisman, R. (1990) A sensitive method for the determination of protein-DNA binding specificities. Nucleic Acids Res., 18, 6197-6204.
47. 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.
48. 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.
49. Robert, F., Douziech, M., Forget, D., Egly, J.M., Grenblatt, J., Burton, Z.F. and Coulombe, B. (1998) Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF. Mol. Cell, 2, 341-351.
50. Roeder, R.G. (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci., 21, 327-335.
51. Ryu, S., Zhou, S., Ladurner, A.G. and Tjian, R. (1999) The transcriptional co-factor complex CRSP is required for activity of the enhancer binding protein Sp1. Nature, 397, 446-450.
52. Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
53. Sawadogo, M. and Roeder, R.G. (1985) Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. Cell, 43, 165-175.
54. Shen, W.-C. and Green, M.R. (1997) Yeast TAFμ145 functions as a core promoter selectivity factor, not a general coactivator. Cell, 90, 615-624.
55. Smale, S.T. (1997) Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes. Biochim. Biophys. Acta. 1351, 73-88.
56. Smale, S.T. and Baltimore, D. (1989) The 'initiator' as a transcription control element. Cell, 57, 103-113.
57. Sypes, M.A. and Gilmour, D.S. (1994) Protein-DNA crosslinking of a TFIID complex reveals novel interactions downstream of the transcription start. Nucleic Acids Res., 22, 807-814.
58. van der Knaap, J.A., Borst, J.W., van der Vliet, P.C., Gentz, R. and Timmers, H.T.M. (1997) Cloning of the cDNA for the TATA-binding protein associated factor(II)70 subunit of transcription factor B-TFIID reveals homology to global transcription regulators in yeast and Drosophila. Proc. Natl Acad. Sci. USA, 94, 11827-11837.
59. Verrijzer, C.P. and Tjian, R. (1996) TAFs mediate transcriptional activation and promoter selectivity. Trends Biochem. Sci., 21, 338-342.
60. II150: Similarity to yeast gene TSM-1 and specific binding to core promoter DNA. Science, 264, 933-941.
61. 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.
62. Wang, J.C. and Van Dyke, M.W. (1993) Initiator sequences direct downstream promoter binding by human transcription factor IID. Biochim. Biophys. Acta, 1216, 73-80.
63. II250-dependent transcription of cyclin A is directed by ATF activator proteins. Genes Dev., 11, 2658-2669.
64. 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.
65. II-containing complex without TBP in transcription by RNA polymerase II. Nature, 393, 187-191.
66. II105 mediates activation of anti-apoptotic genes by NF-κB. EMBO J., 17, 5161-5169.
67. Yokomori, K., Verrijzer, C.P. and Tjian, R. (1998) An interplay between TATA box-binding protein and transcription factors IIE and IIA modulates DNA binding and transcription. Proc. Natl Acad. Sci. USA, 95, 6722-6727.
68. Zhou, Q., Liebermann, P.M., Boyer, T.G. and Berk, A.J. (1992) Holo-TFIID supports transcriptional stimulation by diverse activators and from TATA-less promoters. Genes Dev., 6, 1964-1974.