ArticleGenome biology2012
Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 23 citations in OpenAlex.
- Dynamic 3D chromatin organization and epigenetic regulation of gene expression in peanut nodules.Journal of integrative plant biology · 2025Article
- Altered chromatin architecture and gene expression during polyploidization and domestication of soybean.The Plant cell · 2021Article
- New insights into homoeologous copy number variations in the hexaploid wheat genome.The plant genome · 2021Article
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- Complex Molecular Evolution and Expression of Expansin Gene Families in Three Basic Diploid Species ofInternational journal of molecular sciences · 2020Article
- The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?Genes · 2019Article
- Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation.Genome biology · 2017Article
- Global Regulation of Plant Immunity by Histone Lysine Methyl Transferases.The Plant cell · 2016Article
- Dissecting the complex molecular evolution and expression of polygalacturonase gene family in Brassica rapa ssp. chinensis.Plant molecular biology · 2015Article
- A neutrality test for detecting selection on DNA methylation using single methylation polymorphism frequency spectrum.Genome biology and evolution · 2014Article
- Monoubiquitination of histone 2B at the disease resistance gene locus regulates its expression and impacts immune responses in Arabidopsis.Plant physiology · 2014Article
- The histone modification H3K27me3 is retained after gene duplication and correlates with conserved noncoding sequences in Arabidopsis.Genome biology and evolution · 2014Article
- Accumulation of CTCF-binding sites drives expression divergence between tandemly duplicated genes in humans.BMC genomics · 2014Article
- Article
- Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27.The Plant cell · 2013Article
- The allure of the epigenome.Genome biology · 2012Article
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3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundFollowing gene duplication, retained paralogs undergo functional divergence, which is reflected in changes in DNA sequence and expression patterns. The extent of divergence is influenced by several factors, including protein function. We examine whether an epigenetic modification, trimethylation of histone H3 at lysine 27 (H3K27me3), could be a factor in the evolution of expression patterns after gene duplication. Whereas in animals this repressive mark for transcription is deposited on long regions of DNA, in plants its localization is gene-specific. Because of this and a well-annotated recent whole-genome duplication, Arabidopsis thaliana is uniquely suited for studying the potential association of H3K27me3 with the evolutionary fate of genes.
resultsParalogous pairs with H3K27me3 show the highest coding sequence divergence, which can be explained by their low expression levels. Interestingly, they also show the highest similarity in expression patterns and upstream regulatory regions, while paralogous pairs where only one gene is an H3K27me3 target show the highest divergence in expression patterns and upstream regulatory sequence. These trends in divergence of expression and upstream regions are especially pronounced for transcription factors.
conclusionsAfter duplication, a histone modification can be associated with a particular fate of paralogs: H3K27me3 is linked to lower expression divergence yet higher coding sequence divergence. Our results show that H3K27me3 constrains expression divergence after duplication. Moreover, its association with higher conservation of upstream regions provides a potential mechanism for the conserved H3K27me3 targeting of the paralogs.
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