TY - JOUR

T1 - In situ dissecting the evolution of gene duplication with different histone modification patterns based on high-throughput data analysis in Arabidopsis thaliana

AU - Wang, Jingjing

AU - Orlov, Yuriy L.

AU - Li, Xue

AU - Zhou, Yincong

AU - Liu, Yongjing

AU - Yuan, Chunhui

AU - Chen, Ming

N1 - Publisher Copyright: Copyright 2021 Wang et al.

PY - 2021/1/5

Y1 - 2021/1/5

N2 - Background: Genetic regulation is known to contribute to the divergent expression of duplicate genes; however, little is known about how epigenetic modifications regulate the expression of duplicate genes in plants. Methods: The histone modification (HM) profile patterns of different modes of gene duplication, including the whole genome duplication, proximal duplication, tandem duplication and transposed duplication were characterized based on ChIP-chip or ChIP-seq datasets. In this study, 10 distinct HM marks including H2Bub, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me2, H3K27me1, H3K27me3, H3K36me3 and H3K14ac were analyzed. Moreover, the features of gene duplication with different HM patterns were characterized based on 88 RNA-seq datasets of Arabidopsis thaliana. Results: This study showed that duplicate genes in Arabidopsis have a more similar HM pattern than single-copy genes in both their promoters and protein-coding regions. The evolution of HM marks is found to be coupled with coding sequence divergence and expression divergence after gene duplication. We found that functionally selective constraints may impose on epigenetic evolution after gene duplication. Furthermore, duplicate genes with distinct functions have more divergence in histone modification compared with the ones with the same function, while higher expression divergence is found with mutations of chromatin modifiers.

AB - Background: Genetic regulation is known to contribute to the divergent expression of duplicate genes; however, little is known about how epigenetic modifications regulate the expression of duplicate genes in plants. Methods: The histone modification (HM) profile patterns of different modes of gene duplication, including the whole genome duplication, proximal duplication, tandem duplication and transposed duplication were characterized based on ChIP-chip or ChIP-seq datasets. In this study, 10 distinct HM marks including H2Bub, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me2, H3K27me1, H3K27me3, H3K36me3 and H3K14ac were analyzed. Moreover, the features of gene duplication with different HM patterns were characterized based on 88 RNA-seq datasets of Arabidopsis thaliana. Results: This study showed that duplicate genes in Arabidopsis have a more similar HM pattern than single-copy genes in both their promoters and protein-coding regions. The evolution of HM marks is found to be coupled with coding sequence divergence and expression divergence after gene duplication. We found that functionally selective constraints may impose on epigenetic evolution after gene duplication. Furthermore, duplicate genes with distinct functions have more divergence in histone modification compared with the ones with the same function, while higher expression divergence is found with mutations of chromatin modifiers.

KW - A. thaliana

KW - Bioinformatics

KW - ChIP-chip

KW - Epigenetic pattern evolution

KW - Gene duplication

KW - Histone modifications

KW - Plant genome

KW - RNA-seq

KW - EXPRESSION DIVERGENCE

KW - DNA METHYLATION

KW - TANDEM

KW - MECHANISMS

KW - GENOME

UR - http://www.scopus.com/inward/record.url?scp=85099043126&partnerID=8YFLogxK

U2 - 10.7717/peerj.10426

DO - 10.7717/peerj.10426

M3 - Article

C2 - 33505781

AN - SCOPUS:85099043126

VL - 9

JO - PeerJ

JF - PeerJ

SN - 2167-8359

M1 - e10426

ER -