Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters

Gene

Volumn 389, Issue 1, 2007, Pages 52-65

  Yang, Chuhu ^a   Bolotin, Eugene ^a   Jiang, Tao ^a,b   Sladek, Frances M ^a   Martinez, Ernest ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California Riverside   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Core promoter elements; ELK 1; Genome wide computational analysis; M22; Motif distribution; Sp1; Transcription

Indexed keywords

ARTICLE; DNA DETERMINATION; HUMAN GENOME; PRIORITY JOURNAL; PROMOTER REGION; TATA BOX; TRANSCRIPTION INITIATION SITE; YEAST;

BASE COMPOSITION; BASE SEQUENCE; CONSERVED SEQUENCE; GENOME, FUNGAL; GENOME, HUMAN; HUMANS; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); REGULATORY ELEMENTS, TRANSCRIPTIONAL; TATA BOX; YEASTS;

EUKARYOTA; MAMMALIA; VERTEBRATA;

EID: 33846214719     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2006.09.029     Document Type: Article

References (62)

1. Aerts S., Thijs G., Dabrowski M., Moreau Y., and De Moor B. Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC Genomics 5 (2004) 34-44
2. Aso T., Conaway J.W., and Conaway R.C. 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 (1994) 26575-26583
3. Bajic V.B., Choudhary V., and Hock C.K. Content analysis of the core promoter region of human genes. In Silico Biol. 4 (2004) 109-125
4. Basehoar A.D., Zanton S.J., and Pugh B.F. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116 (2004) 699-709
5. Bazykin G.A., and Kondrashov A.S. Rate of promoter class turn-over in yeast evolution. BMC Evol. Biol. 6 (2006) 14
6. Bucher P. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212 (1990) 563-578
7. Chen W., and Struhl K. Yeast mRNA initiation sites are determined primarily by specific sequences, not by the distance from the TATA element. EMBO J. 4 (1985) 3273-3280
8. Cormen T., Leiserson C., and Riverst R. Introduction to Algorithms (1992), MIT Press, Cambridge
9. David L., et al. A high-resolution map of transcription in the yeast genome. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 5320-5325
10. Deng W., and Roberts S.G.E. A core promoter element downstream of the TATA box that is recognized by TFIIB. Genes Dev. 19 (2005) 2418-2423
11. Dujon B. The yeast genome project: what did we learn?. Trends Genet. 12 (1996) 263-270
12. Fitzgerald P.C., Shlyakhtenko A., Mir A.A., and Vinson C. Clustering of DNA sequences in human promoters. Genome Res. 14 (2004) 1562-1574
13. Gardiner-Garden M., and Frommer M. CpG islands in vertebrate genomes. J. Mol. Biol. 196 (1987) 261-282
14. Gershenzon N.I., and Ioshikhes I.P. Synergy of human Pol II core promoter elements revealed by statistical sequence analysis. Bioinformatics 21 (2005) 1295-1300
15. Green M.R. TBP-associated factors (TAFIIs): multiple, selective transcriptional mediators in common complexes. Trends Biochem. Sci. 25 (2000) 59-63
16. Hahn S. Structure and mechanism of the RNA polymerase II transcription machinery. Nat. Struct. Mol. Biol. 11 (2004) 394-403
17. Hahn S., Hoar E.T., and Guarente L. Each of three "TATA elements" specifies a subset of the transcription initiation sites at the CYC-1 promoter of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 82 (1985) 8562-8566
18. Hahn S., Buratowski S., Sharp P.A., and Guarente L. Yeast TATA-binding protein TFIID binds to TATA elements with both consensus and nonconsensus DNA sequences. Proc. Natl. Acad. Sci. U. S. A. 86 (1989) 5718-5722
19. Hampsey M. Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. Mol. Biol. Rev. 62 (1998) 465-503
20. Hosack D.A., Dennis G., Sherman B.T., Lane H.C., and Lempicki R.A. Identifying biological themes within lists of genes with EASE. Genome Biol. 4 (2003) R60
21. Javahery R., Khachi A., Lo K., Zenzie-Gregory B., and Smale S.T. DNA sequence requirements for transcriptional initiator activity in mammalian cells. Mol. Cell. Biol. 14 (1994) 116-127
22. Jin V.X., Singer G.A., Agosto-Perez F.J., Liyanarachchi S., and Davuluri R.V. Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. BMC Bioinformatics 7 (2006) 114
23. Kel-Margoulis O.V., et al. Composition-sensitive analysis of the human genome for regulatory signals. In Silico Biol. 3 (2003) 145-171
24. Kimura K., et al. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res. 16 (2006) 55-65
25. Kraus R.J., et al. Experimentally determined weight matrix definitions of the initiator and TBP binding site elements of promoters. Nucleic Acids Res. 24 (1996) 1531-1539
26. Kuehner J.N., and Brow D.A. Quantitative analysis of in vivo initiator selection by yeast RNA polymerase II supports a scanning model. J. Biol. Chem. 281 (2006) 14119-14128
27. Kunkel G.R., and Martinson H.G. Nucleosomes will not form on double-stranded RNA or over poly(dA).poly(dT) tracts in recombinant DNA. Nucleic Acids Res. 9 (1981) 6869-6888
28. Kutach A.K., and Kadonaga J.T. The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol. Cell. Biol. 20 (2000) 4754-4764
29. Larsen F., Gundersen G., Lopez R., and Prydz H. CpG islands as gene markers in the human genome. Genomics 13 (1992) 1095-1107
30. Lee C.K., Shibata Y., Rao B., Strahl B.D., and Lieb J.D. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet. 36 (2004) 900-905
31. Lee D.H., Gershenzon N., Gupta M., Ioshikhes I.P., Reinberg D., and Lewis B.A. Functional characterization of core promoter elements: the downstream core element is recognized by TAF1. Mol. Cell. Biol. 25 (2005) 9674-9686
32. Lewis B.A., Sims III R.J., Lane W.S., and Reinberg D. Functional characterization of core promoter elements: DPE-specific transcription requires the protein kinase CK2 and the PC4 coactivator. Mol. Cell 18 (2005) 471-481
33. Lim C.Y., Santoso B., Boulay T., Dong E., Ohler U., and Kadonaga J.T. The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev. 18 (2004) 1606-1617
34. Majewski J., and Ott J. Distribution and characterization of regulatory elements in the human genome. Genome Res. 12 (2002) 1827-1836
35. Martinez E., Chiang C.M., Ge H., and Roeder R.G. 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 (1994) 3115-3126
36. Martinez E., Zhou Q., L'Etoile N.D., Oelgeschlager T., Berk A.J., and Roeder R.G. Core promoter-specific function of a mutant transcription factor TFIID defective in TATA-box binding. Proc. Natl. Acad. Sci. U. S. A. 92 (1995) 11864-11868
37. Martinez E., Ge H., Tao Y., Yuan C.X., Palhan V., and Roeder R.G. Novel cofactors and TFIIA mediate functional core promoter selectivity by the human TAFII150-containing TFIID complex. Mol. Cell. Biol. 18 (1998) 6571-6583
38. Mosch H.U., Graf R., and Braus G.H. Sequence-specific initiator elements focus initiation of transcription to distinct sites in the yeast TRP4 promoter. EMBO J. 11 (1992) 4583-4590
39. Ohler U., Liao G.C., Niemann H., and Rubin G.M. Computational analysis of core promoters in the Drosophila genome. Genome Biol. 3 (2002) research0087.1-0087.12
40. O'Shea-Greenfield A., and Smale S.T. Roles of TATA and initiator elements in determining the start site location and direction of RNA polymerase II transcription. J. Biol. Chem. 267 (1992) 1391-1402
41. Patikoglou G.A., Kim J.L., Sun L., Yang S.H., Kodadek T., and Burley S.K. TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev. 13 (1999) 3217-3230
42. Roeder R.G. Role of general and gene-specific cofactors in the regulation of eukaryotic transcription. Cold Spring Harbor Symp. Quant. Biol. 63 (1998) 201-218
43. Sakurai H., Ohishi T., and Fukasawa T. Two alternative pathways of transcription initiation in the yeast negative regulatory gene GAL80. Mol. Cell. Biol. 14 (1994) 6819-6828
44. Saxonov S., Berg P., and Brutlag D.L. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 1412-1417
45. Schumacher M.A., Lau A.O., and Johnson P.J. Structural basis of core promoter recognition in a primitive eukaryote. Cell 115 (2003) 413-424
46. Sekinger E.A., Moqtaderi Z., and Struhl K. Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol. Cell 18 (2005) 735-748
47. Shimizu M., Mori T., Sakurai T., and Shindo H. Destabilization of nucleosomes by an unusual DNA conformation adopted by poly(dA).poly(dT) tracts in vivo. EMBO J. 19 (2000) 3358-3365
48. Smale S.T., and Kadonaga J.T. The RNA polymerase II core promoter. Annu. Rev. Biochem. 72 (2003) 449-479
49. Singer V.L., Wobbe C.R., and Struhl K. A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation. Genes Dev. 4 (1990) 636-645
50. Suzuki Y., et al. Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Genome Res. 11 (2001) 677-684
51. Suzuki Y., et al. Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep. 2 (2001) 388-393
52. Suzuki Y., Yamashita R., Sugano S., and Nakai K. DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res. 32 (2004) D78-D81
53. Trinklein N.D., Aldred S.J., Saldanha A.J., and Myers R.M. Identification and functional analysis of human transcriptional promoters. Genome Res. 13 (2003) 308-312
54. Weis L., and Reinberg D. 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 (1997) 2973-2984
55. Wiley S.R., Kraus R.J., and Mertz J.E. Functional binding of the "TATA" box binding component of transcription factor TFIID to the - 30 region of TATA-less promoters. Proc. Natl. Acad. Sci. U. S. A. 89 (1992) 5814-5818
56. Willy P.J., Kobayashi R., and Kadonaga J.T. A basal transcription factor that activates or represses transcription. Science 290 (2000) 982-985
57. Wobbe C.R., and Struhl K. Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro. Mol. Cell. Biol. 10 (1990) 3859-3867
58. Xie X., et al. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434 (2005) 338-345
59. Yamashita R., Suzuki Y., Sugano S., and Nakai K. Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene 350 (2005) 129-136
60. Yuan G.C., et al. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309 (2005) 626-630
61. Zenzie-Gregory B., Khachi A., Garraway I.P., and Smale S.T. Mechanism of initiator-mediated transcription: evidence for a functional interaction between the TATA-binding protein and DNA in the absence of a specific recognition sequence. Mol. Cell. Biol. 13 (1993) 3841-3849
62. Zhang Z., and Dietrich F.S. Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res. 33 (2005) 2838-2851