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Open Access Research article

Histone modification pattern evolution after yeast gene duplication

Yangyun Zou1, Zhixi Su1, Wei Huang2 and Xun Gu12*

Author Affiliations

1 Ministry of Education Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China

2 Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA

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BMC Evolutionary Biology 2012, 12:111  doi:10.1186/1471-2148-12-111

Published: 9 July 2012

Abstract

Background

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.

Results

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 cis- and trans-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.

Conclusions

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.

Keywords:
Histone modification; Histone modification code divergence; Gene duplication; Expression divergence; Epigenetic divergence; cis-regulation; trans-regulation