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Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences
Gene regulation differs greatly between related species, constituting a major source of phenotypic diversity. Recent studies characterized extensive differences in the gene expression programs of closely related species. In contrast, virtually nothing is known about the evolution of chromatin struct...
Autores principales: | , , |
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Formato: | Texto |
Lenguaje: | English |
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European Molecular Biology Organization
2010
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890324/ https://www.ncbi.nlm.nih.gov/pubmed/20461072 http://dx.doi.org/10.1038/msb.2010.20 |
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author | Tirosh, Itay Sigal, Nadejda Barkai, Naama |
author_facet | Tirosh, Itay Sigal, Nadejda Barkai, Naama |
author_sort | Tirosh, Itay |
collection | PubMed |
description | Gene regulation differs greatly between related species, constituting a major source of phenotypic diversity. Recent studies characterized extensive differences in the gene expression programs of closely related species. In contrast, virtually nothing is known about the evolution of chromatin structure and how it influences the divergence of gene expression. Here, we compare the genome-wide nucleosome positioning of two closely related yeast species and, by profiling their inter-specific hybrid, trace the genetic basis of the observed differences into mutations affecting the local DNA sequences (cis effects) or the upstream regulators (trans effects). The majority (∼70%) of inter-species differences is due to cis effects, leaving a significant contribution (30%) for trans factors. We show that cis effects are well explained by mutations in nucleosome-disfavoring AT-rich sequences, but are not associated with divergence of nucleosome-favoring sequences. Differences in nucleosome positioning propagate to multiple adjacent nucleosomes, supporting the statistical positioning hypothesis, and we provide evidence that nucleosome-free regions, but not the +1 nucleosome, serve as stable border elements. Surprisingly, although we find that differential nucleosome positioning among cell types is strongly correlated with differential expression, this does not seem to be the case for evolutionary changes: divergence of nucleosome positioning is excluded from regulatory elements and is not correlated with gene expression divergence, suggesting a primarily neutral mode of evolution. Our results provide evolutionary insights to the genetic determinants and regulatory function of nucleosome positioning. |
format | Text |
id | pubmed-2890324 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | European Molecular Biology Organization |
record_format | MEDLINE/PubMed |
spelling | pubmed-28903242010-06-24 Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences Tirosh, Itay Sigal, Nadejda Barkai, Naama Mol Syst Biol Article Gene regulation differs greatly between related species, constituting a major source of phenotypic diversity. Recent studies characterized extensive differences in the gene expression programs of closely related species. In contrast, virtually nothing is known about the evolution of chromatin structure and how it influences the divergence of gene expression. Here, we compare the genome-wide nucleosome positioning of two closely related yeast species and, by profiling their inter-specific hybrid, trace the genetic basis of the observed differences into mutations affecting the local DNA sequences (cis effects) or the upstream regulators (trans effects). The majority (∼70%) of inter-species differences is due to cis effects, leaving a significant contribution (30%) for trans factors. We show that cis effects are well explained by mutations in nucleosome-disfavoring AT-rich sequences, but are not associated with divergence of nucleosome-favoring sequences. Differences in nucleosome positioning propagate to multiple adjacent nucleosomes, supporting the statistical positioning hypothesis, and we provide evidence that nucleosome-free regions, but not the +1 nucleosome, serve as stable border elements. Surprisingly, although we find that differential nucleosome positioning among cell types is strongly correlated with differential expression, this does not seem to be the case for evolutionary changes: divergence of nucleosome positioning is excluded from regulatory elements and is not correlated with gene expression divergence, suggesting a primarily neutral mode of evolution. Our results provide evolutionary insights to the genetic determinants and regulatory function of nucleosome positioning. European Molecular Biology Organization 2010-05-11 /pmc/articles/PMC2890324/ /pubmed/20461072 http://dx.doi.org/10.1038/msb.2010.20 Text en Copyright © 2010, EMBO and Macmillan Publishers Limited https://creativecommons.org/licenses/by-nc-sa/3.0/This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits distribution and reproduction in any medium, provided the original author and source are credited. Creation of derivative works is permitted but the resulting work may be distributed only under the same or similar licence to this one. This licence does not permit commercial exploitation without specific permission. |
spellingShingle | Article Tirosh, Itay Sigal, Nadejda Barkai, Naama Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences |
title | Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences |
title_full | Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences |
title_fullStr | Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences |
title_full_unstemmed | Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences |
title_short | Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences |
title_sort | divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890324/ https://www.ncbi.nlm.nih.gov/pubmed/20461072 http://dx.doi.org/10.1038/msb.2010.20 |
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