Whole-genome discovery of transcription factor binding sites by network-level conservation

Genome Research

Volumn 14, Issue 1, 2004, Pages 99-108

  Pritsker, Moshe ^a   Liu, Yir Chung ^a   Beer, Michael A ^a   Tavazoie, Saeed ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; CONSERVATION GENETICS; CONTROLLED STUDY; EUKARYOTE; GENE EXPRESSION PROFILING; GENE MAPPING; GENE SEQUENCE; GENETIC ALGORITHM; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN MOTIF; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; BASE COMPOSITION; BINDING SITES; CONSERVED SEQUENCE; CONTIG MAPPING; DNA, FUNGAL; GENOME, FUNGAL; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; PREDICTIVE VALUE OF TESTS; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION FACTORS;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 0347135946     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1739204     Document Type: Article

References (35)

1. Altschul, S., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. Proc. Natl. Acad. Sci. 87: 5509-5513.
2. Aparicio, S., Morrison, A., Gould, A., Gilthorpe, J., Chaudhuri, C., Rigby, P., Krumlauf R., and Brenner, S. 1995. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc. Natl. Acad. Sci. 92: 1684-1688.
3. Blanchette, M. and Tompa, M. 2002. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12: 739-748.
4. Bussemaker, H., Li, H., and Siggia, E.D. 2001. Regulatory element detection using correlation with expression. Nat. Genet. 27: 167-171.
5. Causton, H.C., Ren, B., Koh, S.S., Harbison, C.T., Kanin, E., Jennings, E.G., Lee, T.I., True, H.L., Lander, E.S., and Young, R.A. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell 12: 323-337.
6. Cho, R.J., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockhart, D.J., et al. 1998. A genome wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2: 65-73.
7. Cliften, P., Hillier, L.W., Fulton, L., Graves, T., Miner, T., Gish, W.R., Waterston, R.H., and Johnston, M. 2001. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res. 11: 1175-1186.
8. Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen B.A., and Johnston M. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
9. Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. 95: 14863-14868.
10. Gilligan, P., Brenner, S., and Venkatesh, B. 2002. Fugu and human sequence comparison identifies novel human genes and conserved non-coding sequences. Gene 294: 35-44.
11. Gumucio, D.L., Heilstedt-Williamson, H., Gray, T.A., Tarle, S.A., Shelton, D.A., Tagle, D.A., Slightom, J.L., Goodman, M., and Collins, F.S. 1992. Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human γ and ε globin genes. Mol. Cell Biol. 12: 4919-4929.
12. Hill, D.P., Blake, J.A., Richardson, J.E., and Ringwald, M. 2002. Extension and integration of the gene ontology (GO): Combining GO vocabularies with external vocabularies. Genome Res. 12: 1982-1991.
13. Hughes, J.D., Estep, P.W., Tavazoie, S., and Church, G.M. 2000. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296: 1205-1214.
14. Hughes, T.R., Marton, M.J., Jones, A.R., Roberts, C.J., Stoughton, R., Armour, C.D., Bennett, H.A., Coffey, E., Dai, H., He, Y.D., et al. 2000. Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
15. Jelinsky, S.A., Estep, P., Church, G.M., and Samson, L.D. 2000. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: RPN4 links base excision repair with proteasome. Moll. Cell. Biol. 20: 8157-8167.
16. Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
17. Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F., and Wootton, J.C. 1993. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science 262: 208-214.
18. Lee, T.I., Rinaldi, N.J., Roberts, F., Odom, D., Bar-Joseph, Z., and Gerber, G.K. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
19. Li, H., Rhodius, V., Gross, C., and Siggia, E.D. 2002. Identification of the binding sites of regulatory proteins in bacterial genomes. Proc. Natl. Acad. Sci. 99: 11772-11777.
20. McCue, L., Thompson, W., Carmack, C., Ryan, M.P., Liu, J.S., Derbyshire, V., and Lawrence, C.E. 2001. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res. 29: 774-782.
21. McGuire, A.M., Hughes, J.D., and Church, G.M. 2000. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 10: 744-757.
22. Mewes, H.W., Frishman, D., Guldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., Morgenstern, B., Munsterkotter, M., Rudd, S., and Weil, B. 2002. MIPS: A database for genomes and protein sequences. Nucleic Acids Res. 30: 31-34.
23. Neuwald, A.F., Liu, J.S., and Lawrence, C.E. 199S. Gibbs motif sampling: Detection of bacterial outer membrane protein repeats. Protein Sci. 4: 1618-1632.
24. Oshima, Y. 1997. The phosphatase system in Saccharomyces cerevisiae. Genes Genet. Syst. 72: 323-334.
25. Rajewsky, N., Socci, N.D., Zapotocky, M., and Siggia, E.D. 2002. The evolution of DNA regulatory regions for proteo-γ bacteria by interspecies comparisons. Genome Res. 12: 298-308.
26. Roth, F.P., Hughes, J.D., Estep, P.W., and Church, G.M. 1998. Finding DNA-regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol. 16: 949-945.
27. Schneider, T.D. and Stephens, R.M. 1990. Sequence logos: A new way to display consensus sequences. Nucleic Acids Res. 18: 6097-6100.
28. Souciet, J., Aigle, M., Artiguenave, F., Blandin, G., Bolotin-Fukuhara, M., Bon, E., Brottier, P., Casaregola, S., de Montigny, J., Dujon, B., et al. 2000. Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies. FEBS Lett. 487: 3-12.
29. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D., and Futcher, B. 1998. Comprehensive indentification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization, Mol. Biol. Cell 9: 3273-3297.
30. Stormo, G. and Fields, D. 1998. Specificity, free energy and information content in protein-DNA interactions. Trends Biochem. Sci. 23: 109-113.
31. Sudarsanam, P., Pilpel, Y., and Church, G.M. 2002. Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res. 12: 1723-1731.
32. Tagle D.A., Koop B.F., Goodman M., Slightom J.L., Hess D.L., and Jones R.T. 1988. Embryonic E and γ globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 203: 439-455.
33. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J., and Church, G.M. 1999. Systematic determination of genetic network architecture. Nat. Genet. 22: 281-285.
34. Thompson, J., Higgins D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
35. Xie, Y. and Varshavsky, A. 2001. RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: A negative feedback circuit. Proc. Natl. Acad. Sci. 98: 3056-3061.