Flexible promoter architecture requirements for coactivator recruitment

BMC Molecular Biology

Volumn 7, Issue , 2006, Pages

  Chiang, Derek Y ^a,d   Nix, David A ^b,e   Shultzaberger, Ryan K ^a   Gasch, Audrey P ^c   Eisen, Michael B ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

^d BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^e Thermo Fisher Scientific   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CBF1; TRANSCRIPTION FACTOR MET31; TRANSCRIPTION FACTOR MET32; TRANSCRIPTION FACTOR MET4; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; FUNGAL GENE; FUNGAL GENETICS; FUNGAL STRAIN; GENE EXPRESSION; GENE SEQUENCE; GENETIC TRANSCRIPTION; NONHUMAN; PREDICTION; PROTEIN BINDING; REPORTER GENE; SACCHAROMYCES CEREVISIAE;

BASIC HELIX-LOOP-HELIX LEUCINE ZIPPER TRANSCRIPTION FACTORS; BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS; BINDING SITES; GENE EXPRESSION REGULATION, FUNGAL; GENE LIBRARY; MODELS, GENETIC; PLASMIDS; PROMOTER REGIONS, GENETIC; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS;

EID: 33745834749     PISSN: 14712199     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-7-16     Document Type: Article

References (49)

1. Carey M: The enhanceosome and transcriptional synergy. Cell 1998, 92:5-8.
2. Merika M, Thanos D: Enhanceosomes. Curr Opin Genet Dev 2001, 11:205-208.
3. Ogata K, Sato K, Tahirov TH: Eukaryotic transcriptional regulatory complexes: cooperativity from near and afar. Curr Opin Struct Biol 2003, 13:40-48.
4. Remenyi A, Scholer HR, Wimanns M: Combinatorial control of gene expression. Nat Struct Mol Biol 2004, 11:812-817.
5. van Helden J, Rios AF, Collado-Vides J: Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res 2000, 28:1808-1818.
6. GuhaThakurta D, Stormo GD: Identifying target sites for cooperatively binding factors. Bioinformatics 2001, 17:608-621.
7. Liu X, Brutlag DL, Liu JS: BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 2001, 6:127-138.
8. Robin S, Daudin JJ, Richard H, Sagot MF, Schbath S: Occurrence probability of structured motifs in random sequences. J Comput Biol 2002, 9:761-773.
9. Klingenhoff A, Frech K, Quandt K, Werner T: Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity. Bioinformatics 1999, 15:180-186.
10. Pilpel Y, Sudarsanam P, Church GM: Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 2001, 29:153-159.
11. Bulyk MJ, McGuire AM, Masuda N, Church GM: A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. Genome Res 2004, 14:201-208.
12. Amin J, Fernandez M, Ananthan J, Lis JT, Voellmy R: Cooperative binding of heat shock transcription factor to the Hsp70 promoter in vivo and in vitro. J Biol Chem 1994, 269:4804-4811.
13. Drazinic CM, Smerage JB, Lopez MC, Baker HV: Activation mechanism of the multifunctional transcription factor repressoractivator protein 1 (Rap1p). Mol Cell Biol 1996, 16:3187-3196.
14. Brazas RM, Bhoite LT, Murphy MD, Yu Y, Chen Y, Neklason DW, Stillman DJ: Determining the requirements for cooperative DNA binding by Swi5p and Pho2p (Grf10p/Bas2p) at the HO promoter. J Biol Chem 1995, 270:29151-29161.
15. Jin Y, Mead J, Li T, Wolberger C, Vershon AK: Altered DNA recognition and bending by insertions in the α2 tail of the yeast a1/α2 homeodomain heterodimer. Science 1995, 270:290-292.
16. Ioshikhes I, Trifonov EN, Zhang MQ: Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proc Natl Acad Sci USA 1999, 96:2891-2895.
17. Makeev VJ, Lifanov AP, Nazina AG, Papatsenko DA: Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. Nucleic Acids Res 2003, 31:6016-6026.
18. Naar AM, Lemon BD, Tjian R: Transcriptional coactivator complexes. Annu Rev Biochem 2001, 70:475-501.
19. Spiegelman BM, Heinrich R: Biological control through regulated transcriptional coactivators. Cell 2004, 119:157-167.
20. Kuras L, Barbey R, Thomas D: Assembly of a bZIP-bHLH transcription activation complex: Formation of the yeast Cbf1-Met4-Met28 complex is regulated through Met28 stimulation of Cbf1 DNA binding. EMBO J 1997, 16:2441-2451.
21. Blaiseau PL, Thomas D: Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA. EMBO J 1998, 17:6327-6336.
22. Kuras L, Cherest H, Surdin-Kerjan Y, Thomas D: A heteromeric complex containing the centromere binding factor 1 and two basic leucine zipper factors, Met4 and Met28, mediates the transcription activation of yeast sulfur metabolism. EMBO J 1996, 15:2519-2529.
23. Thomas D, Surdin-Kerjan Y: Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 1997, 61:503-532.
24. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254.
25. Melcher K, Sharma B, Ding WV, Nolden M: Zero background yeast reporter plasmids. Gene 2000, 247:53-61.
26. Horecka J, Sprague GFJ: Use of imadazoleglyercerolphosphate dehydratase (His3) as a biological reporter in yeast. Methods Enzymol 2000, 326:107-119.
27. Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA: Dissecting the regulatory circuitry of a eukaryotic genome. Cell 1998, 95:717-728.
28. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 2000, 11:4241-4257.
29. Fauchon M, Lagniel G, Aude JC, Lombardia L, Soularue P, Petat C, Marguerie G, Sentenac A, Werner M, Labarre J: Sulfur sparing in the yeast proteome in response to sulfur demand. Mol Cell 2002, 9:713-723.
30. Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: A sequence logo generator. Genome Res 2004, 14:1188-1190.
31. Schneider TD, Stephens RM: Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 1990, 18:6097-6100.
32. Niedenthal RK, Sen-Gupta M, Wilmen A, Hegemann JH: Cpf1 protein induced bending of yeast centromere DNA element I. Nucleic Acids Res 1993, 21:4726-4733.
33. Lim FL, Hayes A, West AG, Pic-Taylor A, Darieva Z, Morgan BA, Oliver SG, Sharrocks AD: Mcm1p-induced DNA bending regulates the formation of ternary transcription factor complexes. Mol Cell Biol 2003, 23:450-461.
34. Elledge SJ, Davis RW: Position and density effects on repression by stationary and mobile DNA-binding proteins. Genes Dev 1989, 3:185-197.
35. Mai X, Chou S, Struhl K: Preferential accessibility of the yeast HIS3 promoter is determined by a general property of the DNA sequence, not by specific elements. Mol Cell Biol 2000, 20:6668-6676.
36. Tornoe J, Kusk P, Johansen TE, Jensen PR: Generation of a synthetic mammalian promoter library by modification of sequences spacing transcription factor binding sites. Gene 2002, 297:21-32.
37. Olson WK, Gorin AA, Lu X-J, Hock LM, Zhurkin VB: DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA 1998, 95:11163-11168.
38. Moreau JL, Lee M, Mahachi N, Vary J, Mellor J, Tsukiyama T, Goding CR: Regulated displacement of TBP from the PHO8 promoter in vivo requires Cbf1 and the Isw1 chromatin remodeling complex. Mol Cell 2003, 11(6):1609-1620.
39. Kent NA, Eibert SM, Mellor J: Cbf1p is required for chromatin remodeling at promoter-proximal CACGTG motifs in yeast. J Biol Chem 2004, 279(26):27116-27123.
40. Futcher B: Transcriptional regulatory networks and the yeast cell cycle. Curr Opin Cell Biol 2002, 14(6):676-683.
41. Istrail S, Davidson EH: Logic functions of the genomic cis-regulatory code. Proc Natl Acad Sci USA 2005, 102:4954-4959.
42. Wagner A: Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics 1999, 15:776-784.
43. Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB: Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol 2003, 4:R43.
44. Beer MA, Tavazoie S: Predicting gene expression from sequence. Cell 2004, 117:185-198.
45. Sikorski RS, Hieter P: A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 1989, 122:19-27.
46. Gueldener U, Heinisch J, Koehler GJ, Voss D, Hegemann JH: A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast. Nucleic Acids Res 2002, 30:e23.
47. Gietz RD, Woods RA: Transformation of yeast by lithium acetate/ single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol 2002, 350:87-96.
48. Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM: Fungal BLAST and model organism BLASTP best hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res 2005, 33:D374-D377.
49. Cliften PF, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston RH, Cohen BA, Johnston M: Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 2003, 301:71-76.