Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation

Genome Biology
Claudia ChicaFrancois Roudier

Abstract

Polycomb Repressive Complexes 2 (PRC2) are multi-protein chromatin modifiers that are evolutionarily conserved among eukaryotes and play key roles in the regulation of gene expression, notably through the trimethylation of lysine 27 of histone H3 (H3K27me3). Although PRC2-mediated gene regulation has been studied in many organisms, few studies have explored in depth the evolutionary conservation of PRC2 targets. Here, we compare the H3K27me3 epigenomic profiles for the two closely related species Arabidopsis thaliana and Arabidopsis lyrata and the more distant species Arabis alpina, three Brassicaceae that diverged from each other within the past 24 million years. Using a robust set of gene orthologs present in the three species, we identify two classes of evolutionarily conserved PRC2 targets, which are characterized by either developmentally plastic or developmentally constrained H3K27me3 marking across species. Constrained H3K27me3 marking is associated with higher conservation of promoter sequence information content and higher nucleosome occupancy compared to plastic H3K27me3 marking. Moreover, gene orthologs with constrained H3K27me3 marking exhibit a higher degree of tissue specificity and tend to be involved in developm...Continue Reading

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Citations

Aug 1, 2018·Nature Plants·Ezgi Süheyla Doğan, Chang Liu
Jan 27, 2021·Current Opinion in Plant Biology·Naseem SamoIva Mozgová
Nov 2, 2020·The Plant Journal : for Cell and Molecular Biology·Yanfeng LiuQingxin Song

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Datasets Mentioned

BETA
GSE50636

Methods Mentioned

BETA
immunoprecipitation
Hi-C
ChIP-seq
Hi-C-seq

Software Mentioned

GenomicusPlants
Phylogeny Inference Package ( PHYLIP )
PhylDiag
EnsemblCompara
ohnolog
Tomtom
ohnologs
agriGO Plant GO slim
Ensembl
BlastP

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