Explicit equilibrium modeling of transcription-factor binding and gene regulation

Genome Biology

Volumn 6, Issue 10, 2005, Pages

  Granek, Joshua A ^a,b   Clarke, Neil D ^a,c  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NATIONAL EVOLUTIONARY SYNTHESIS CENTER   (United States)

^c GENOME INSTITUTE OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; FORKHEAD TRANSCRIPTION FACTOR; NDT80 PROTEIN, S CEREVISIAE; NUCLEAR PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; SUM1 PROTEIN, S CEREVISIAE; TRANSCRIPTION FACTOR;

ARTICLE; BINDING COMPETITION; BIOLOGICAL MODEL; CHROMATIN IMMUNOPRECIPITATION; DNA MICROARRAY; GENE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PROMOTER REGION; PROTEIN BINDING;

BINDING, COMPETITIVE; CHROMATIN IMMUNOPRECIPITATION; DNA-BINDING PROTEINS; FORKHEAD TRANSCRIPTION FACTORS; GENE EXPRESSION REGULATION; GENES, CDC; MODELS, GENETIC; NUCLEAR PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS;

EID: 34548087820     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2005-6-10-r87     Document Type: Article

References (39)

1. DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278:680-686.
2. Hughes JD, Estep PW, Tavazoie S, Church GM: Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 2000, 296:1205-1214.
3. Liu X, Clarke ND: Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities. J Mol Biol 2002, 323:1-8.
4. Beer MA, Tavazoie S: Predicting gene expression from sequence. Cell 2004, 117:185-198.
5. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I: The transcriptional program of sporulation in budding yeast. Science 1998, 282:699-705.
6. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO: Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 2001, 409:533-538.
7. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9:3273-3297.
8. Schneider TD: Information content of individual genetic sequences. J Theor Biol 1997, 189:427-441.
9. Stormo GD, Fields DS: Specificity, free energy and information content in protein-DNA interactions. Trends Biochem Sci 1998, 23:109-113.
10. Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, Davis TN, Futcher B: Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 2000, 406:90-94.
11. Hollenhorst PC, Pietz G, Fox CA: Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: implications for regulating the cell cycle and differentiation. Genes Dev 2001, 15:2445-2456.
12. Pierce M, Benjamin KR, Montano SP, Georgiadis MM, Winter E, Vershon AK: Sum1 and Ndt80 proteins compete for binding to middle sporulation element sequences that control meiotic gene expression. Mol Cell Biol 2003, 23:4814-4825.
13. Lieb JD, Liu X, Botstein D, Brown PO: Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 2001, 28:327-334.
14. Hanley JA, McNeil BJ: The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 1982, 143:29-36.
15. Clarke ND, Granek JA: Rank order metrics for quantifying the association of sequence features with gene regulation. Bioinformatics 2003, 19:212-218.
16. Roth FP, Hughes JD, Estep PW, Church GM: Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 1998, 16:939-945.
17. Boros J, Lim FL, Darieva Z, Pic-Taylor A, Harman R, Morgan BA, Sharrocks AD: Molecular determinants of the cell-cycle regulated Mcm1p-Fkh2p transcription factor complex. Nucleic Acids Res 2003, 31:2279-2288.
18. Miller JA, Widom J: Collaborative competition mechanism for gene activation in vivo. Mol Cell Biol 2003, 23:1623-1632.
19. Hepworth SR, Friesen H, Segall J: NDT80 and the meiotic recombination checkpoint regulate expression of middle sporulation- specific genes in Saccharomyces cerevisiae. Mol Cell Biol 1998, 18:5750-5761.
20. Xie J, Pierce M, Gailus-Durner V, Wagner M, Winter E, Vershon AK: Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae. EMBO J 1999, 18:6448-6454.
21. Wang W, Cherry JM, Nochomovitz Y, Jolly E, Botstein D, Li H: Inference of combinatorial regulation in yeast transcriptional networks:a case study of sporulation. Proc Natl Acad Sci USA 2005, 102:1998-2003.
22. Djordjevic M, Sengupta AM, Shraiman BI: A biophysical approach to transcription factor binding site discovery. Genome Res 2003, 13:2381-2390.
23. Liu X, Noll DM, Lieb JD, Clarke ND: DIP-chip: Rapid and accurate determination of DNA-binding specificity. Genome Res 2005, 15:421-427.
24. Markstein M, Markstein P, Markstein V, Levine MS: Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc Natl Acad Sci USA 2002, 99:763-768.
25. Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB: Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci USA 2002, 99:757-762.
26. Rebeiz M, Reeves NL, Posakony JW: SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Site clustering over random expectation. Proc Natl Acad Sci USA 2002, 99:9888-9893.
27. Hertz GZ, Stormo GD: Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15:563-577.
28. Carroll KL, Pradhan DA, Granek JA, Clarke ND, Corden JL: Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts. Mol Cell Biol 2004, 24:6241-6252.
29. Oliphant AR, Brandl CJ, Struhl K: Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol Cell Biol 1989, 9:2944-2949.
30. Liu X, Brutlag DL, Liu JS: BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 2001:127-138.
31. Conlon EM, Liu XS, Lieb JD, Liu JS: Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci USA 2003, 100:3339-3344.
32. Benos PV, Bulyk ML, Stormo GD: Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res 2002, 30:4442-4451.
33. Murtin C, Engelhorn M, Geiselmann J, Boccard F: A quantitative UV laser footprinting analysis of the interaction of IHF with specific binding sites: re-evaluation of the effective concentration of IHF in the cell. J Mol Biol 1998, 284:949-961.
34. Saccharomyces Genome Database [ftp://ftp.yeastgenome.org/ yeast/]
35. van Rossum G, de Boer J: Interactively testing remote servers using the python programming language. CWI Quarterly 1991, 4:283-303.
36. GOMER [http://biophysics.med.jhmi.edu/clarke/granek/GOMER/]
37. Schneider TD, Stephens RM: Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 1990, 18:6097-6100.
38. Wynne J, Treisman R: SRF and MCM1 have related but distinct DNA binding specificities. Nucleic Acids Res 1992, 20:3297-3303.
39. Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16:276-277.