Transcriptional regulatory code of a eukaryotic genome (original) (raw)
References
Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol.3, 318–356 (1961) ArticleCAS Google Scholar
Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature423, 241–254 (2003) ArticleADSCAS Google Scholar
Cliften, P. et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science301, 71–76 (2003) ArticleADSCAS Google Scholar
Pritsker, M., Liu, Y. C., Beer, M. A. & Tavazoie, S. Whole-genome discovery of transcription factor binding sites by network-level conservation. Genome Res.14, 99–108 (2004) ArticleCAS Google Scholar
Wang, T. & Stormo, G. D. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics19, 2369–2380 (2003) ArticleCAS Google Scholar
Blanchette, M. & Tompa, M. FootPrinter: A program designed for phylogenetic footprinting. Nucleic Acids Res.31, 3840–3842 (2003) ArticleCAS Google Scholar
Iyer, V. R. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature409, 533–538 (2001) ArticleADSCAS Google Scholar
Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science290, 2306–2309 (2000) ArticleADSCAS Google Scholar
Lee, T. I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science298, 799–804 (2002) ArticleADSCAS Google Scholar
Lieb, J. D., Liu, X., Botstein, D. & Brown, P. O. Promoter-specific binding of Rap1 revealed by genome–wide maps of protein-DNA association. Nature Genet.28, 327–334 (2001) ArticleCAS Google Scholar
Roth, F. P., Hughes, J. D., Estep, P. W. & Church, G. M. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnol.16, 939–945 (1998) ArticleCAS Google Scholar
Liu, X. S., Brutlag, D. L. & Liu, J. S. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nature Biotechnol.20, 835–839 (2002) ArticleCAS Google Scholar
Bailey, T. L. & Elkan, C. Proc. Int. Conf. Intell. Syst. Mol. Biol.Vol. 3 21–29 (AAAI Press, Menlo Park, California, 1995) Google Scholar
Knuppel, R., Dietze, P., Lehnberg, W., Frech, K. & Wingender, E. TRANSFAC retrieval program: a network model database of eukaryotic transcription regulating sequences and proteins. J. Comput. Biol.1, 191–198 (1994) ArticleCAS Google Scholar
Cunningham, T. S. & Cooper, T. G. The Saccharomyces cerevisiae DAL80 repressor protein binds to multiple copies of GATAA-containing sequences (URSGATA). J. Bacteriol.175, 5851–5861 (1993) ArticleCAS Google Scholar
Donahue, T. F., Daves, R. S., Lucchini, G. & Fink, G. R. A short nucleotide sequence required for regulation of HIS4 by the general control system of yeast. Cell32, 89–98 (1983) ArticleCAS Google Scholar
Kirkpatrick, C. R. & Schimmel, P. Detection of leucine-independent DNA site occupancy of the yeast Leu3p transcriptional activator in vivo. Mol. Cell. Biol.15, 4021–4030 (1995) ArticleCAS Google Scholar
Axelrod, J. D., Majors, J. & Brandriss, M. C. Proline-independent binding of PUT3 transcriptional activator protein detected by footprinting in vivo. Mol. Cell. Biol.11, 564–567 (1991) ArticleCAS Google Scholar
Ma, J. & Ptashne, M. The carboxy-terminal 30 amino acids of GAL4 are recognized by GAL80. Cell50, 137–142 (1987) ArticleCAS Google Scholar
Beck, T. & Hall, M. N. The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature402, 689–692 (1999) ArticleADSCAS Google Scholar
Chi, Y. et al. Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev.15, 1078–1092 (2001) ArticleCAS Google Scholar
Albrecht, G., Mosch, H. U., Hoffmann, B., Reusser, U. & Braus, G. H. Monitoring the Gcn4 protein-mediated response in the yeast Saccharomyces cerevisiae. J. Biol. Chem.273, 12696–12702 (1998) ArticleCAS Google Scholar
Kornitzer, D., Raboy, B., Kulka, R. G. & Fink, G. R. Regulated degradation of the transcription factor Gcn4. EMBO J.13, 6021–6030 (1994) ArticleCAS Google Scholar
Zeitlinger, J. et al. Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell113, 395–404 (2003) ArticleCAS Google Scholar
Baur, M., Esch, R. K. & Errede, B. Cooperative binding interactions required for function of the Ty1 sterile responsive element. Mol. Cell. Biol.17, 4330–4337 (1997) ArticleCAS Google Scholar
Waterston, R. H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature420, 520–562 (2002) ArticleADSCAS Google Scholar
Matys, V. et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res.31, 374–378 (2003) ArticleCAS Google Scholar
Hodges, P. E., McKee, A. H., Davis, B. P., Payne, W. E. & Garrels, J. I. The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data. Nucleic Acids Res.27, 69–73 (1999) ArticleCAS Google Scholar
Zhu, J. & Zhang, M. Q. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics15, 607–611 (1999) ArticleCAS Google Scholar
Schneider, T. D. & Stephens, R. M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res.18, 6097–6100 (1990) ArticleCAS Google Scholar