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Epigenetic modifications are associated with inter-species gene expression variation in primates

BACKGROUND: Changes in gene regulation have long been thought to play an important role in evolution and speciation, especially in primates. Over the past decade, comparative genomic studies have revealed extensive inter-species differences in gene expression levels, yet we know much less about the...

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Autores principales: Zhou, Xiang, Cain, Carolyn E, Myrthil, Marsha, Lewellen, Noah, Michelini, Katelyn, Davenport, Emily R, Stephens, Matthew, Pritchard, Jonathan K, Gilad, Yoav
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290387/
https://www.ncbi.nlm.nih.gov/pubmed/25468404
http://dx.doi.org/10.1186/s13059-014-0547-3
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author Zhou, Xiang
Cain, Carolyn E
Myrthil, Marsha
Lewellen, Noah
Michelini, Katelyn
Davenport, Emily R
Stephens, Matthew
Pritchard, Jonathan K
Gilad, Yoav
author_facet Zhou, Xiang
Cain, Carolyn E
Myrthil, Marsha
Lewellen, Noah
Michelini, Katelyn
Davenport, Emily R
Stephens, Matthew
Pritchard, Jonathan K
Gilad, Yoav
author_sort Zhou, Xiang
collection PubMed
description BACKGROUND: Changes in gene regulation have long been thought to play an important role in evolution and speciation, especially in primates. Over the past decade, comparative genomic studies have revealed extensive inter-species differences in gene expression levels, yet we know much less about the extent to which regulatory mechanisms differ between species. RESULTS: To begin addressing this gap, we perform a comparative epigenetic study in primate lymphoblastoid cell lines, to query the contribution of RNA polymerase II and four histone modifications, H3K4me1, H3K4me3, H3K27ac, and H3K27me3, to inter-species variation in gene expression levels. We find that inter-species differences in mark enrichment near transcription start sites are significantly more often associated with inter-species differences in the corresponding gene expression level than expected by chance alone. Interestingly, we also find that first-order interactions among the five marks, as well as chromatin states, do not markedly contribute to the degree of association between the marks and inter-species variation in gene expression levels, suggesting that the marginal effects of the five marks dominate this contribution. CONCLUSIONS: Our observations suggest that epigenetic modifications are substantially associated with changes in gene expression levels among primates and may represent important molecular mechanisms in primate evolution. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0547-3) contains supplementary material, which is available to authorized users.
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spelling pubmed-42903872015-01-28 Epigenetic modifications are associated with inter-species gene expression variation in primates Zhou, Xiang Cain, Carolyn E Myrthil, Marsha Lewellen, Noah Michelini, Katelyn Davenport, Emily R Stephens, Matthew Pritchard, Jonathan K Gilad, Yoav Genome Biol Research BACKGROUND: Changes in gene regulation have long been thought to play an important role in evolution and speciation, especially in primates. Over the past decade, comparative genomic studies have revealed extensive inter-species differences in gene expression levels, yet we know much less about the extent to which regulatory mechanisms differ between species. RESULTS: To begin addressing this gap, we perform a comparative epigenetic study in primate lymphoblastoid cell lines, to query the contribution of RNA polymerase II and four histone modifications, H3K4me1, H3K4me3, H3K27ac, and H3K27me3, to inter-species variation in gene expression levels. We find that inter-species differences in mark enrichment near transcription start sites are significantly more often associated with inter-species differences in the corresponding gene expression level than expected by chance alone. Interestingly, we also find that first-order interactions among the five marks, as well as chromatin states, do not markedly contribute to the degree of association between the marks and inter-species variation in gene expression levels, suggesting that the marginal effects of the five marks dominate this contribution. CONCLUSIONS: Our observations suggest that epigenetic modifications are substantially associated with changes in gene expression levels among primates and may represent important molecular mechanisms in primate evolution. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0547-3) contains supplementary material, which is available to authorized users. BioMed Central 2014-12-03 /pmc/articles/PMC4290387/ /pubmed/25468404 http://dx.doi.org/10.1186/s13059-014-0547-3 Text en © Zhou et al.; licensee BioMed Central. 2014 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Zhou, Xiang
Cain, Carolyn E
Myrthil, Marsha
Lewellen, Noah
Michelini, Katelyn
Davenport, Emily R
Stephens, Matthew
Pritchard, Jonathan K
Gilad, Yoav
Epigenetic modifications are associated with inter-species gene expression variation in primates
title Epigenetic modifications are associated with inter-species gene expression variation in primates
title_full Epigenetic modifications are associated with inter-species gene expression variation in primates
title_fullStr Epigenetic modifications are associated with inter-species gene expression variation in primates
title_full_unstemmed Epigenetic modifications are associated with inter-species gene expression variation in primates
title_short Epigenetic modifications are associated with inter-species gene expression variation in primates
title_sort epigenetic modifications are associated with inter-species gene expression variation in primates
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290387/
https://www.ncbi.nlm.nih.gov/pubmed/25468404
http://dx.doi.org/10.1186/s13059-014-0547-3
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