Transcriptional regulatory code of a eukaryotic genome (original) (raw)

References

  1. Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318–356 (1961)
    Article CAS Google Scholar
  2. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241–254 (2003)
    Article ADS CAS Google Scholar
  3. Cliften, P. et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301, 71–76 (2003)
    Article ADS CAS Google Scholar
  4. 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)
    Article CAS Google Scholar
  5. Wang, T. & Stormo, G. D. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 19, 2369–2380 (2003)
    Article CAS Google Scholar
  6. Blanchette, M. & Tompa, M. FootPrinter: A program designed for phylogenetic footprinting. Nucleic Acids Res. 31, 3840–3842 (2003)
    Article CAS Google Scholar
  7. Iyer, V. R. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533–538 (2001)
    Article ADS CAS Google Scholar
  8. Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306–2309 (2000)
    Article ADS CAS Google Scholar
  9. Lee, T. I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799–804 (2002)
    Article ADS CAS Google Scholar
  10. 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)
    Article CAS Google Scholar
  11. 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)
    Article CAS Google Scholar
  12. 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)
    Article CAS Google Scholar
  13. Bailey, T. L. & Elkan, C. Proc. Int. Conf. Intell. Syst. Mol. Biol. Vol. 3 21–29 (AAAI Press, Menlo Park, California, 1995)
    Google Scholar
  14. 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)
    Article CAS Google Scholar
  15. 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)
    Article CAS Google Scholar
  16. 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. Cell 32, 89–98 (1983)
    Article CAS Google Scholar
  17. 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)
    Article CAS Google Scholar
  18. 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)
    Article CAS Google Scholar
  19. Ma, J. & Ptashne, M. The carboxy-terminal 30 amino acids of GAL4 are recognized by GAL80. Cell 50, 137–142 (1987)
    Article CAS Google Scholar
  20. Beck, T. & Hall, M. N. The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature 402, 689–692 (1999)
    Article ADS CAS Google Scholar
  21. Chi, Y. et al. Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev. 15, 1078–1092 (2001)
    Article CAS Google Scholar
  22. 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)
    Article CAS Google Scholar
  23. Kornitzer, D., Raboy, B., Kulka, R. G. & Fink, G. R. Regulated degradation of the transcription factor Gcn4. EMBO J. 13, 6021–6030 (1994)
    Article CAS Google Scholar
  24. Zeitlinger, J. et al. Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell 113, 395–404 (2003)
    Article CAS Google Scholar
  25. 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)
    Article CAS Google Scholar
  26. Waterston, R. H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002)
    Article ADS CAS Google Scholar
  27. Matys, V. et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374–378 (2003)
    Article CAS Google Scholar
  28. 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)
    Article CAS Google Scholar
  29. Zhu, J. & Zhang, M. Q. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15, 607–611 (1999)
    Article CAS Google Scholar
  30. Schneider, T. D. & Stephens, R. M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18, 6097–6100 (1990)
    Article CAS Google Scholar

Download references