Transcription control reprogramming in genetic backup circuits (original) (raw)

References

  1. Conant, G.C. & Wagner, A. Duplicate genes and robustness to transient gene knock-downs in Caenorhabditis elegans. Proc. R. Soc. Lond. B Biol. Sci. 271, 89–96 (2004).
    Article Google Scholar
  2. Gu, Z. et al. Role of duplicate genes in genetic robustness against null mutations. Nature 421, 63–66 (2003).
    Article CAS PubMed Google Scholar
  3. Nowak, M.A., Boerlijst, M.C., Cooke, J. & Smith, J.M. Evolution of genetic redundancy. Nature 388, 167–171 (1997).
    Article CAS PubMed Google Scholar
  4. Lynch, M., O'Hely, M., Walsh, B. & Force, A. The probability of preservation of a newly arisen gene duplicate. Genetics 159, 1789–1804 (2001).
    CAS PubMed PubMed Central Google Scholar
  5. Lynch, M. & Conery, J.S. The evolutionary fate and consequences of duplicate genes. Science 290, 1151–1155 (2000).
    Article CAS PubMed Google Scholar
  6. Force, A. et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531–1545 (1999).
    CAS PubMed PubMed Central Google Scholar
  7. Wagner, A. The role of population size, pleiotropy and fitness effects of mutations in the evolution of overlapping gene functions. Genetics 154, 1389–1401 (2000).
    CAS PubMed PubMed Central Google Scholar
  8. Gu, Z., Nicolae, D., Lu, H.H. & Li, W.H. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 18, 609–613 (2002).
    Article CAS PubMed Google Scholar
  9. Huh, W.K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003).
    Article CAS PubMed Google Scholar
  10. Papp, B., Pal, C. & Hurst, L.D. Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet. 19, 417–422 (2003).
    Article CAS PubMed Google Scholar
  11. van den Berg, M.A. et al. The two acetyl-coenzyme A synthetases of Saccharomyces cerevisiae differ with respect to kinetic properties and transcriptional regulation. J. Biol. Chem. 271, 28953–28959 (1996).
    Article CAS PubMed Google Scholar
  12. Kratzer, S. & Schuller, H.J. Transcriptional control of the yeast acetyl-CoA synthetase gene, ACS1, by the positive regulators CAT8 and ADR1 and the pleiotropic repressor UME6. Mol. Microbiol. 26, 631–641 (1997).
    Article CAS PubMed Google Scholar
  13. Hughes, T.R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109–126 (2000).
    Article CAS PubMed Google Scholar
  14. Jansen, R., Greenbaum, D. & Gerstein, M. Relating whole-genome expression data with protein-protein interactions. Genome Res. 12, 37–46 (2002).
    Article CAS PubMed PubMed Central Google Scholar
  15. Ge, H., Liu, Z., Church, G.M. & Vidal, M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat. Genet. 29, 482–486 (2001).
    Article CAS PubMed Google Scholar
  16. Lynch, M. & Katju, V. The altered evolutionary trajectories of gene duplicates. Trends Genet. 20, 544–549 (2004).
    Article CAS PubMed Google Scholar
  17. Teichmann, S.A. & Babu, M.M. Gene regulatory network growth by duplication. Nat. Genet. 36, 492–496 (2004).
    Article CAS PubMed Google Scholar
  18. Kondrashov, F.A., Rogozin, I.B., Wolf, Y.I. & Koonin, E.V. Selection in the evolution of gene duplications. Genome Biol. 3, RESEARCH0008 (2002).
    Article PubMed PubMed Central Google Scholar
  19. Papp, B., Pal, C. & Hurst, L.D. Metabolic network analysis of the causes and evolution of enzyme 'dispensability' in yeast. Nature 429, 661–664 (2004).
    Article CAS PubMed Google Scholar
  20. 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 CAS PubMed Google Scholar
  21. Goldman, N. & Yang, Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11, 725–736 (1994).
    CAS PubMed Google Scholar
  22. Cavalcanti, A.R., Ferreira, R., Gu, Z. & Li, W.H. Patterns of gene duplication in Saccharomyces cerevisiae and Caenorhabditis elegans. J. Mol. Evol. 56, 28–37 (2003).
    Article CAS PubMed Google Scholar
  23. Steinmetz, L.M. et al. Systematic screen for human disease genes in yeast. Nat. Genet. 31, 400–404 (2002).
    Article CAS PubMed Google Scholar
  24. Harbison, C.T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99–104 (2004).
    Article CAS PubMed PubMed Central Google Scholar
  25. Pilpel, Y., Sudarsanam, P. & Church, G.M. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29, 153–159 (2001).
    Article CAS PubMed Google Scholar
  26. Kellis, M., Birren, B.W. & Lander, E.S. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428, 617–624 (2004).
    Article CAS PubMed Google Scholar
  27. Lord, P.W., Stevens, R.D., Brass, A. & Goble, C.A. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19, 1275–1283 (2003).
    Article CAS PubMed Google Scholar
  28. Ozcan, S. Two different signals regulate repression and induction of gene expression by glucose. J. Biol. Chem. 277, 46993–46997 (2002).
    Article CAS PubMed Google Scholar
  29. McCammon, M.T. & McAlister-Henn, L. Multiple cellular consequences of isocitrate dehydrogenase isozyme dysfunction. Arch. Biochem. Biophys. 419, 222–233 (2003).
    Article CAS PubMed Google Scholar
  30. Garcia-Rodriguez, L.J. et al. Characterization of the chitin biosynthesis process as a compensatory mechanism in the fks1 mutant of Saccharomyces cerevisiae. FEBS Lett. 478, 84–88 (2000).
    Article CAS PubMed Google Scholar

Download references