Histone modification pattern evolution after yeast gene duplication

<p>Abstract</p> <p>Background</p> <p>Gene duplication and subsequent functional divergence especially expression divergence have been widely considered as main sources for evolutionary innovations. Many studies evidenced that genetic regulatory network evolved rapidly s...

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Main Authors: Zou Yangyun, Su Zhixi, Huang Wei, Gu Xun
Format: Article
Language:English
Published: BMC 2012-07-01
Series:BMC Evolutionary Biology
Subjects:
Online Access:http://www.biomedcentral.com/1471-2148/12/111
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spelling doaj-2258dd3aaba64f3b97cea169e6435f0b2021-09-02T03:02:59ZengBMCBMC Evolutionary Biology1471-21482012-07-0112111110.1186/1471-2148-12-111Histone modification pattern evolution after yeast gene duplicationZou YangyunSu ZhixiHuang WeiGu Xun<p>Abstract</p> <p>Background</p> <p>Gene duplication and subsequent functional divergence especially expression divergence have been widely considered as main sources for evolutionary innovations. Many studies evidenced that genetic regulatory network evolved rapidly shortly after gene duplication, thus leading to accelerated expression divergence and diversification. However, little is known whether epigenetic factors have mediated the evolution of expression regulation since gene duplication. In this study, we conducted detailed analyses on yeast histone modification (HM), the major epigenetics type in this organism, as well as other available functional genomics data to address this issue.</p> <p>Results</p> <p>Duplicate genes, on average, share more common HM-code patterns than random singleton pairs in their promoters and open reading frames (ORF). Though HM-code divergence between duplicates in both promoter and ORF regions increase with their sequence divergence, the HM-code in ORF region evolves slower than that in promoter region, probably owing to the functional constraints imposed on protein sequences. After excluding the confounding effect of sequence divergence (or evolutionary time), we found the evidence supporting the notion that in yeast, the HM-code may co-evolve with <it>cis</it>- and <it>trans</it>-regulatory factors. Moreover, we observed that deletion of some yeast HM-related enzymes increases the expression divergence between duplicate genes, yet the effect is lower than the case of transcription factor (TF) deletion or environmental stresses.</p> <p>Conclusions</p> <p>Our analyses demonstrate that after gene duplication, yeast histone modification profile between duplicates diverged with evolutionary time, similar to genetic regulatory elements. Moreover, we found the evidence of the co-evolution between genetic and epigenetic elements since gene duplication, together contributing to the expression divergence between duplicate genes.</p> http://www.biomedcentral.com/1471-2148/12/111Histone modificationHistone modification code divergenceGene duplicationExpression divergenceEpigenetic divergence<it>cis</it>-regulation<it>trans</it>-regulation
collection DOAJ
language English
format Article
sources DOAJ
author Zou Yangyun
Su Zhixi
Huang Wei
Gu Xun
spellingShingle Zou Yangyun
Su Zhixi
Huang Wei
Gu Xun
Histone modification pattern evolution after yeast gene duplication
BMC Evolutionary Biology
Histone modification
Histone modification code divergence
Gene duplication
Expression divergence
Epigenetic divergence
<it>cis</it>-regulation
<it>trans</it>-regulation
author_facet Zou Yangyun
Su Zhixi
Huang Wei
Gu Xun
author_sort Zou Yangyun
title Histone modification pattern evolution after yeast gene duplication
title_short Histone modification pattern evolution after yeast gene duplication
title_full Histone modification pattern evolution after yeast gene duplication
title_fullStr Histone modification pattern evolution after yeast gene duplication
title_full_unstemmed Histone modification pattern evolution after yeast gene duplication
title_sort histone modification pattern evolution after yeast gene duplication
publisher BMC
series BMC Evolutionary Biology
issn 1471-2148
publishDate 2012-07-01
description <p>Abstract</p> <p>Background</p> <p>Gene duplication and subsequent functional divergence especially expression divergence have been widely considered as main sources for evolutionary innovations. Many studies evidenced that genetic regulatory network evolved rapidly shortly after gene duplication, thus leading to accelerated expression divergence and diversification. However, little is known whether epigenetic factors have mediated the evolution of expression regulation since gene duplication. In this study, we conducted detailed analyses on yeast histone modification (HM), the major epigenetics type in this organism, as well as other available functional genomics data to address this issue.</p> <p>Results</p> <p>Duplicate genes, on average, share more common HM-code patterns than random singleton pairs in their promoters and open reading frames (ORF). Though HM-code divergence between duplicates in both promoter and ORF regions increase with their sequence divergence, the HM-code in ORF region evolves slower than that in promoter region, probably owing to the functional constraints imposed on protein sequences. After excluding the confounding effect of sequence divergence (or evolutionary time), we found the evidence supporting the notion that in yeast, the HM-code may co-evolve with <it>cis</it>- and <it>trans</it>-regulatory factors. Moreover, we observed that deletion of some yeast HM-related enzymes increases the expression divergence between duplicate genes, yet the effect is lower than the case of transcription factor (TF) deletion or environmental stresses.</p> <p>Conclusions</p> <p>Our analyses demonstrate that after gene duplication, yeast histone modification profile between duplicates diverged with evolutionary time, similar to genetic regulatory elements. Moreover, we found the evidence of the co-evolution between genetic and epigenetic elements since gene duplication, together contributing to the expression divergence between duplicate genes.</p>
topic Histone modification
Histone modification code divergence
Gene duplication
Expression divergence
Epigenetic divergence
<it>cis</it>-regulation
<it>trans</it>-regulation
url http://www.biomedcentral.com/1471-2148/12/111
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