Evolutionary footprints of nucleosome positions in yeast - PubMed (original) (raw)
Evolutionary footprints of nucleosome positions in yeast
Stefan Washietl et al. Trends Genet. 2008 Dec.
Abstract
Using genome-wide maps of nucleosome positions in yeast, we have analyzed the influence of chromatin structure on the molecular evolution of genomic DNA. We have observed, on average, 10-15% lower substitution rates in linker regions than in nucleosomal DNA. This widespread local rate heterogeneity represents an evolutionary footprint of nucleosome positions and reveals that nucleosome organization is a genomic feature conserved over evolutionary timescales.
Similar articles
- Genome-scale identification of nucleosome positions in S. cerevisiae.
Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. Yuan GC, et al. Science. 2005 Jul 22;309(5734):626-30. doi: 10.1126/science.1112178. Epub 2005 Jun 16. Science. 2005. PMID: 15961632 - Inferring natural selection on fine-scale chromatin organization in yeast.
Babbitt GA, Kim Y. Babbitt GA, et al. Mol Biol Evol. 2008 Aug;25(8):1714-27. doi: 10.1093/molbev/msn127. Epub 2008 May 29. Mol Biol Evol. 2008. PMID: 18515262 - Purification and nucleosome mapping analysis of native yeast plasmid chromatin.
Kim Y, Shen CH, Clark DJ. Kim Y, et al. Methods. 2004 May;33(1):59-67. doi: 10.1016/j.ymeth.2003.10.021. Methods. 2004. PMID: 15039088 - [Organization and evolution of the yeast Saccharomyces cerevisiae genome and the problem of orphan open reading frames].
Mackiewicz P. Mackiewicz P. Postepy Biochem. 2000;46(4):291-8. Postepy Biochem. 2000. PMID: 11449963 Review. Polish. No abstract available. - Nucleosomal organization and DNA base composition patterns.
García A, González S, Antequera F. García A, et al. Nucleus. 2017 Sep 3;8(5):469-474. doi: 10.1080/19491034.2017.1337611. Epub 2017 Jun 21. Nucleus. 2017. PMID: 28635365 Free PMC article. Review.
Cited by
- Drosophila functional elements are embedded in structurally constrained sequences.
Kenigsberg E, Tanay A. Kenigsberg E, et al. PLoS Genet. 2013 May;9(5):e1003512. doi: 10.1371/journal.pgen.1003512. Epub 2013 May 30. PLoS Genet. 2013. PMID: 23750124 Free PMC article. - Fundamental concepts in genetics: genetics and the understanding of selection.
Hurst LD. Hurst LD. Nat Rev Genet. 2009 Feb;10(2):83-93. doi: 10.1038/nrg2506. Nat Rev Genet. 2009. PMID: 19119264 Review. - The impact of the nucleosome code on protein-coding sequence evolution in yeast.
Warnecke T, Batada NN, Hurst LD. Warnecke T, et al. PLoS Genet. 2008 Nov;4(11):e1000250. doi: 10.1371/journal.pgen.1000250. Epub 2008 Nov 7. PLoS Genet. 2008. PMID: 18989456 Free PMC article. - Nucleosomes are well positioned in exons and carry characteristic histone modifications.
Andersson R, Enroth S, Rada-Iglesias A, Wadelius C, Komorowski J. Andersson R, et al. Genome Res. 2009 Oct;19(10):1732-41. doi: 10.1101/gr.092353.109. Epub 2009 Aug 17. Genome Res. 2009. PMID: 19687145 Free PMC article. - Nucleosomal context of binding sites influences transcription factor binding affinity and gene regulation.
Dai Z, Dai X, Xiang Q, Feng J. Dai Z, et al. Genomics Proteomics Bioinformatics. 2009 Dec;7(4):155-62. doi: 10.1016/S1672-0229(08)60045-5. Genomics Proteomics Bioinformatics. 2009. PMID: 20172488 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases