Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays (original) (raw)

References

1. Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 (1995).
   Article CAS PubMed Google Scholar
2. Wodicka, L., Dong, H., Mittmann, M., Ho, M.H. & Lockhart, D.J. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 15, 1359–1367 (1997).
   Article CAS PubMed Google Scholar
3. Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306–2309 (2000).
   Article CAS PubMed Google Scholar
4. Iyer, V.R. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533–538 (2001).
   Article CAS PubMed Google Scholar
5. Lieb, J.D., Liu, X., Botstein, D. & Brown, P.O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28, 327–334 (2001).
   Article CAS PubMed Google Scholar
6. Lee, T. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799–804 (2002).
   Article CAS PubMed Google Scholar
7. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627 (2000).
   Article CAS PubMed Google Scholar
8. MacBeath, G. & Schreiber, S.L. Printing proteins as microarrays for high-throughput function determination. Science 289, 1760–1763 (2000).
   CAS PubMed Google Scholar
9. Ito, T. et al. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. USA 97, 1143–1147 (2000).
   Article CAS PubMed PubMed Central Google Scholar
10. Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180–183 (2002).
    Article CAS PubMed Google Scholar
11. Bulyk, M.L., Huang, X., Choo, Y. & Church, G.M. Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. USA 98, 7158–7163 (2001).
    Article CAS PubMed PubMed Central Google Scholar
12. Linnell, J. et al. Quantitative high-throughput analysis of transcription factor binding specificities. Nucleic Acids Res. 32, e44 (2004).
    Article PubMed PubMed Central Google Scholar
13. Planta, R.J. Regulation of ribosome synthesis in yeast. Yeast 13, 1505–1518 (1997).
    Article CAS PubMed Google Scholar
14. Konig, P., Giraldo, R., Chapman, L. & Rhodes, D. The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. Cell 85, 125–136 (1996).
    Article CAS PubMed Google Scholar
15. Lutfiyya, L.L. et al. Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae. Genetics 150, 1377–1391 (1998).
    CAS PubMed PubMed Central Google Scholar
16. Liu, X., Brutlag, D. & Liu, J. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput. 2001, 127–138 (2001).
    Google Scholar
17. Hughes, J.D., Estep, P.W., Tavazoie, S. & Church, G.M. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296, 1205–1214 (2000).
    Article CAS PubMed Google Scholar
18. Wingender, E. et al. TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res. 28, 316–319 (2000).
    Article CAS PubMed PubMed Central Google Scholar
19. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241–254 (2003).
    Article CAS PubMed Google Scholar
20. Cliften, P. et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301, 71–76 (2003).
    Article CAS PubMed Google Scholar
21. Robison, K., McGuire, A.M. & Church, G.M. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol. 284, 241–254 (1998).
    Article CAS PubMed Google Scholar
22. Tavazoie, S., Hughes, J., Campbell, M., Cho, R. & Church, G. Systematic determination of genetic network architecture. Nat. Genet. 22, 281–285 (1999).
    Article CAS PubMed Google Scholar
23. Drees, B.L. et al. A protein interaction map for cell polarity development. J. Cell. Biol. 154, 549–571 (2001).
    Article CAS PubMed PubMed Central Google Scholar
24. Beer, M.A. & Tavazoie, S. Predicting gene expression from sequence. Cell 117, 185–198 (2004).
    Article CAS PubMed Google Scholar
25. Tsujimoto, Y., Izawa, S. & Inoue, Y. Cooperative regulation of DOG2, encoding 2-deoxyglucose-6-phosphate phosphatase, by Snf1 kinase and the high-osmolarity glycerol-mitogen-activated protein kinase cascade in stress responses of Saccharomyces cerevisiae. J. Bacteriol. 182, 5121–5126 (2000).
    Article CAS PubMed PubMed Central Google Scholar
26. Zaragoza, O., Vincent, O. & Gancedo, J.M. Regulatory elements in the FBP1 promoter respond differently to glucose-dependent signals in Saccharomyces cerevisiae. Biochem. J. 359, 193–201 (2001).
    Article CAS PubMed PubMed Central Google Scholar
27. Griggs, D.W. & Johnston, M. Regulated expression of the GAL4 activator gene in yeast provides a sensitive genetic switch for glucose repression. Proc. Natl. Acad. Sci. USA 88, 8597–8601 (1991).
    Article CAS PubMed PubMed Central Google Scholar
28. Grauslund, M., Lopes, J.M. & Ronnow, B. Expression of GUT1, which encodes glycerol kinase in Saccharomyces cerevisiae, is controlled by the positive regulators Adr1p, Ino2p and Ino4p and the negative regulator Opi1p in a carbon source-dependent fashion. Nucleic Acids Res. 27, 4391–4398 (1999).
    Article CAS PubMed PubMed Central Google Scholar
29. Ozcan, S. & Johnston, M. Function and regulation of yeast hexose transporters. Microbiol. Mol. Biol. Rev. 63, 554–569 (1999).
    CAS PubMed PubMed Central Google Scholar
30. Bojunga, N. & Entian, K.D. Cat8p the activator of gluconeogenic genes in Saccharomyces cerevisiae, regulates carbon source-dependent expression of NADP-dependent cytosolic isocitrate dehydrogenase (Idp2p) and lactate permease (Jen1p). Mol. Gen. Genet. 262, 869–875 (1999).
    Article CAS PubMed Google Scholar
31. Jiang, R. & Carlson, M. The Snf1 protein kinase and its activating subunit, Snf4, interact with distinct domains of the Sip1/Sip2/Gal83 component in the kinase complex. Mol. Cell. Biol. 17, 2099–2106 (1997).
    Article CAS PubMed PubMed Central Google Scholar
32. Palecek, S.P., Parikh, A.S., Huh, J.H. & Kron, S.J. Depression of Saccharomyces cerevisiae invasive growth on non-glucose carbon sources requires the Snf1 kinase. Mol. Microbiol. 45, 453–469 (2002).
    Article CAS PubMed Google Scholar
33. Rae, F.K. et al. Analysis of complementary expression profiles following WT1 induction versus repression reveals the cholesterol/fatty acid synthetic pathways as a possible major target of WT1. Oncogene 23, 3067–3079 (2004).
    Article CAS PubMed Google Scholar
34. Harbison, C.T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99–104 (2004).
    Article CAS PubMed PubMed Central Google Scholar
35. Hartemink, A., Gifford, D., Jaakkola, T. & Young, R. Combining location and expression data for principled discovery of genetic regulatory network models. Pac. Symp. Biocomput. 2002, 437–449 (2002).
    Google Scholar
36. Doi, N. et al. Novel fluorescence labeling and high-throughput assay technologies for in vitro analysis of protein interactions. Genome Res. 12, 487–492 (2002).
    Article CAS PubMed PubMed Central Google Scholar
37. Man, T.K. & Stormo, G.D. Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res. 29, 2471–2478 (2001).
    Article CAS PubMed PubMed Central Google Scholar
38. Bulyk, M., Johnson, P. & Church, G. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res. 30, 1255–1261 (2002).
    Article CAS PubMed PubMed Central Google Scholar
39. Udalova, I., Mott, R., Field, D. & Kwiatkowski, D. Quantitative prediction of NF-kappa B DNA-protein interactions. Proc. Natl. Acad. Sci. USA 99, 8167–8172 (2002).
    Article CAS PubMed PubMed Central Google Scholar
40. Desjarlais, J.R. & Berg, J.M. Toward rules relating zinc finger protein sequences and DNA binding site preferences. Proc. Natl. Acad. Sci. USA 89, 7345–7349 (1992).
    Article CAS PubMed PubMed Central Google Scholar
41. Philippakis, A., He, F. & Bulyk, M. ModuleFinder: a tool for computational discovery of cis regulatory modules. Pac. Symp. Biocomput. (in the press).
42. Zhu, H. et al. Global analysis of protein activities using proteome chips. Science 26, 2101–2105 (2001).
    Article Google Scholar
43. Dudley, A., Aach, J., Steffen, M. & Church, G. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. USA 99, 7554–7559 (2002).
    Article CAS PubMed PubMed Central Google Scholar
44. Cleveland, W. & Devlin, S. Locally weighted regression: An approach to regression analysis by local fitting. J. Am. Stat. Assoc. 83, 596–610 (1988).
    Article Google Scholar
45. Sokal, R. & Rohlf, R. Biometry: The Principles and Practice of Statistics in Biological Research (W. H. Freeman and Company, New York, 1995).
    Google Scholar
46. Liu, X., Brutlag, D. & Liu, J. An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 20, 835–839 (2002).
    Article CAS PubMed Google Scholar
47. Robinson, M., Grigull, J., Mohammad, N. & Hughes, T. FunSpec: a web-based cluster interpreter for yeast. BMC Bioinformatics 3, 35 (2002).
    Article PubMed PubMed Central Google Scholar
48. Stuart, J.M., Segal, E., Koller, D. & Kim, S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 302, 249–255 (2003).
    Article CAS PubMed Google Scholar
49. Schneider, T.D. & Stephens, R.M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18, 6097–6100 (1990).
    Article CAS PubMed PubMed Central Google Scholar

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