Evolution of nucleosome occupancy: Conservation of global properties and divergence of gene-specific patterns

Molecular and Cellular Biology

Volumn 31, Issue 21, 2011, Pages 4348-4355

  Tsui, Kyle ^a,b   Dubuis, Sébastien ^c,d   Gebbia, Marinella ^a   Morse, Randall H ^e   Barkai, Naama ^c   Tirosh, Itay ^c   Nislow, Corey ^a,f  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^d EPFL   (Switzerland)

^e WADSWORTH CENTER   (United States)

^f Banting and Best Department of Medical Research   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANDIDA ALBICANS; CANDIDA GLABRATA; FUNGAL GENE; GENE EXPRESSION; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; SACCHAROMYCES; SACCHAROMYCES BAYANUS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES KUDRIAVZEVII;

CANDIDA GLABRATA; DNA, FUNGAL; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GENETIC DRIFT; GENOME, FUNGAL; GENOME-WIDE ASSOCIATION STUDY; NUCLEOSOMES; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 83255187902     PISSN: 02707306     EISSN: 10985549     Source Type: Journal    
DOI: 10.1128/MCB.05276-11     Document Type: Article

References (45)

1. Babbitt, G. A., and Y. Kim. 2008. Inferring natural selection on fine-scale chromatin organization in yeast. Mol. Biol. Evol. 25:1714-1727.
2. Badis, G., et al. 2008. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol. Cell 32:878-887.
3. Basehoar, A. D., S. J. Zanton, and B. F. Pugh. 2004. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116:699-709.
4. Borneman, A. R., et al. 2007. Divergence of transcription factor binding sites across related yeast species. Science 317:815-819.
5. Cairns, B. R. 2009. The logic of chromatin architecture and remodelling at promoters. Nature 461:193-198.
6. Cantor, C., and T. Jukes. 1969. Mammalian protein metabolism, p. 21- 132. In H. N. Munro (ed.), Evolution of protein molecules. Academic Press, New York, NY.
7. Chan, E. T., et al. 2009. Conservation of core gene expression in vertebrate tissues. J. Biol. 8:33.
8. Cliften, P., et al. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301:71-76.
9. Dujon, B., et al. 2004. Genome evolution in yeasts. Nature 430:35-44.
10. Field, Y., et al. 2009. Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nat. Genet. 41:438- 445.
11. Field, Y., et al. 2008. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput. Biol. 4:e1000216.
12. Fisher, S., E. A. Grice, R. M. Vinton, S. L. Bessling, and A. S. McCallion. 2006. Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 312:276-279.
13. Ganapathi, M., et al. 2011. Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast. Nucleic Acids Res. 39:2032-2044.
14. Gasch, A. P., et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11:4241-4257.
15. Hartley, P. D., and H. D. Madhani. 2009. Mechanisms that specify promoter nucleosome location and identity. Cell 137:445-458.
16. Ihmels, J., et al. 2005. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 309:938-940.
17. Ihmels, J., et al. 2002. Revealing modular organization in the yeast transcriptional network. Nat. Genet. 31:370-377.
18. Jiang, C., and B. F. Pugh. 2009. Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 10:161-172.
19. Kaplan, N., et al. 2009. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458:362-366.
20. Kornberg, R. D., and L. Stryer. 1988. Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism. Nucleic Acids Res. 16:6677-6690.
21. Lee, W., et al. 2007. A high-resolution atlas of nucleosome occupancy in yeast. Nat. Genet. 39:1235-1244.
22. Li, B., M. Carey, and J. L. Workman. 2007. The role of chromatin during transcription. Cell 128:707-719.
23. Liko, D., M. G. Slattery, and W. Heideman. 2007. Stb3 binds to ribosomal RNA processing element motifs that control transcriptional responses to growth in Saccharomyces cerevisiae. J. Biol. Chem. 282:26623-26628.
24. Ludwig, M. Z., N. H. Patel, and M. Kreitman. 1998. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. Development 125:949-958.
25. Mavrich, T. N., et al. 2008. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res. 18:1073-1083.
26. Mavrich, T. N., et al. 2008. Nucleosome organization in the Drosophila genome. Nature 453:358-362.
27. Odom, D. T., et al. 2007. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat. Genet. 39:730-732.
28. Roetzer, A., et al. 2008. Candida glabrata environmental stress response involves Saccharomyces cerevisiae Msn2/4 orthologous transcription factors. Mol. Microbiol. 69:603-620.
29. Romano, L. A., and G. A. Wray. 2003. Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation. Development 130:4187-4199.
30. Ruvinsky, I., and G. Ruvkun. 2003. Functional tests of enhancer conservation between distantly related species. Development 130:5133-5142.
31. Takahashi, H., Y. Mitani, G. Satoh, and N. Satoh. 1999. Evolutionary alterations of the minimal promoter for notochord-specific Brachyury expression in ascidian embryos. Development 126:3725-3734.
32. Tillo, D., and T. R. Hughes. 2009. GC content dominates intrinsic nucleosome occupancy. BMC Bioinformatics 10:442.
33. Tirosh, I., and N. Barkai. 2008. Two strategies for gene regulation by promoter nucleosomes. Genome Res. 18:1084-1091.
34. Tirosh, I., N. Barkai, and K. J. Verstrepen. 2009. Promoter architecture and the evolvability of gene expression. J. Biol. 8:95.
35. Tirosh, I., J. Berman, and N. Barkai. 2007. The pattern and evolution of yeast promoter bendability. Trends Genet. 23:318-321.
36. Tirosh, I., Y. Bilu, and N. Barkai. 2007. Comparative biology: beyond sequence analysis. Curr. Opin. Biotechnol. 18:371-377.
37. Tirosh, I., N. Sigal, and N. Barkai. 2010. Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences. Mol. Syst. Biol. 6:365.
38. Tirosh, I., A. Weinberger, D. Bezalel, M. Kaganovich, and N. Barkai. 2008. On the relation between promoter divergence and gene expression evolution. Mol. Syst. Biol. 4:159.
39. Tsankov, A. M., D. A. Thompson, A. Socha, A. Regev, and O. J. Rando. 2010. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol. 8:e1000414.
40. Wang, Q. F., et al. 2007. Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons. Genome Biol. 8:R1.
41. Wapinski, I., A. Pfeffer, N. Friedman, and A. Regev. 2007. Natural history and evolutionary principles of gene duplication in fungi. Nature 449:54-61.
42. Weiner, A., A. Hughes, M. Yassour, O. J. Rando, and N. Friedman. 2010. High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res. 20:90-100.
43. Whitehouse, I., O. J. Rando, J. Delrow, and T. Tsukiyama. 2007. Chromatin remodelling at promoters suppresses antisense transcription. Nature 450: 1031-1035.
44. Yuan, G. C., et al. 2005. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309:626-630.
45. Zhang, Z., et al. 2011. A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 332:977-980.