Genome‐wide occupancy of histone H3K27 methyltransferases <scp>CURLY LEAF</scp> and <scp>SWINGER</scp> in <i>Arabidopsis</i> seedlings

Abstract

The Polycomb Group (PcG) proteins form two protein complexes, PcG Repressive Complex 1 (PRC1) and PRC2, which are key epigenetic regulators in eukaryotes. PRC2 represses gene expression by catalyzing the trimethylation of histone H3 lysine 27 (H3K27me3). In <i>Arabidopsis</i> (<i>Arabidopsis thaliana</i>), CURLY LEAF (CLF) and SWINGER (SWN) are two major H3K27 methyltransferases and core components of PRC2, playing essential roles in plant growth and development. Despite their importance, genome-wide binding profiles of CLF and SWN have not been determined and compared yet. In this study, we generated transgenic lines expressing GFP-tagged CLF/SWN under their respective native promoters and used them for ChIP-seq analyses to profile the genome-wide distributions of CLF and SWN in <i>Arabidopsis</i> seedlings. We also profiled and compared the global H3K27me3 levels in wild-type (WT) and PcG mutants (<i>clf</i>, <i>swn</i>, and <i>clf swn</i>). Our data show that CLF and SWN bind to almost the same set of genes, except that SWN has a few hundred more targets. Two short DNA sequences, the <i>GAGA</i>-like and <i>Telo</i>-box-like motifs, were found enriched in the CLF and SWN binding regions. The H3K27me3 levels in <i>clf</i>, but not in <i>swn</i>, were markedly reduced compared with WT; and the mark was undetectable in the <i>clf swn</i> double mutant. Further, we profiled the transcriptomes in <i>clf</i>, <i>swn</i>, and <i>clf swn,</i> and compared that with WT. Thus this work provides a useful resource for the plant epigenetics community for dissecting the functions of PRC2 in plant growth and development.