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

Jingjing Wang, Yuriy L. Orlov, Xue Li, Yincong Zhou, Yongjing Liu, Chunhui Yuan, Ming Chen

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Article numbere10426
Number of pages19
JournalPeerJ
Volume9
DOIs
Publication statusPublished - 5 Jan 2021

Keywords

  • A. thaliana
  • Bioinformatics
  • ChIP-chip
  • Epigenetic pattern evolution
  • Gene duplication
  • Histone modifications
  • Plant genome
  • RNA-seq
  • EXPRESSION DIVERGENCE
  • DNA METHYLATION
  • TANDEM
  • MECHANISMS
  • GENOME

OECD FOS+WOS

  • 1.06.KM GENETICS & HEREDITY
  • 3.01.RU NEUROSCIENCES
  • 1.06.CQ BIOCHEMISTRY & MOLECULAR BIOLOGY

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