Genome‐wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings

Abstract

The Polycomb Group (PcG) proteins form two protein complexes, PcG Repressive Complex 1 ( PRC 1) and PRC 2, which are key epigenetic regulators in eukaryotes. PRC 2 represses gene expression by catalyzing the trimethylation of histone H3 lysine 27 (H3K27me3). In Arabidopsis ( Arabidopsis thaliana ), CURLY LEAF ( CLF ) and SWINGER ( SWN ) are two major H3K27 methyltransferases and core components of PRC 2, 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 Ch IP ‐seq analyses to profile the genome‐wide distributions of CLF and SWN in Arabidopsis seedlings. We also profiled and compared the global H3K27me3 levels in wild‐type ( WT ) and PcG mutants ( clf , swn , and clf swn ). 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 GAGA ‐like and Telo ‐box‐like motifs, were found enriched in the CLF and SWN binding regions. The H3K27me3 levels in clf , but not in swn , were markedly reduced compared with WT ; and the mark was undetectable in the clf swn double mutant. Further, we profiled the transcriptomes in clf , swn , and clf swn, and compared that with WT . Thus this work provides a useful resource for the plant epigenetics community for dissecting the functions of PRC 2 in plant growth and development.

HSI2/VAL1 and HSL1/VAL2 function redundantly to regulate seed dormancy by controllingDOG1expression in Arabidopsis

“…Finally, ChIP-qPCR analysis in Ihp1 mutant seedlings showed significant reductions in H3K27me3 chromatin marks across the DOG1 locus, relative to WT (Figure 7F). Shu et al (2019) reported that CLF, a histone methyltransferase component of PRC2, accumulated at FLC, AGL15 and DOG1 genes that are directly regulated by HSI2 (Qüesta et al, 2016; Yuan et al, 2016; Chen et al, 2018). We used BiFC and CoIP assays to confirm that CLF interacts with HSI2 and HSL1 in vivo (Figure 7G) and ChIP-qPCR analysis of H3K27me3 deposition in clf28 mutant seedlings showed significant decreases of this histone mark at P1, C1 and C2 regions of the DOG1 locus compared to WT (Figure 7H).…”

RNA polymerase II-independent recruitment of SPT6L at transcription start sites in Arabidopsis

“…ChIP was performed as previously described (17,20) with minor modifications. For each biological replicate, five grams of 10-day-old Arabidopsis seedlings (one gram for spt6l and spt6l SPT6LΔSH2-GFP seedlings), grown on \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\frac{1}{2}$\end{document} MS medium, were collected.…”

Inhibition of Polycomb Repressive Complex 2 activity reduces trimethylation of H3K27 and affects development in Arabidopsis seedlings

“…Our study does not indicate whether inhibition of methylation is specific for a particular H3K27me3 methyltransferase of the Arabidopsis E(z) group, namely CLF, SWN or MEA, although our data concern the seed-to-seedling transition where CLF and/or SWN are active [11]. Previous genome-wide analyses comparing the global H3K27me3 profile in clf-28 or clf-29 mutant seedlings, which revealed a decreased level of H3K27me3 in the mutant lines compared to the wild-type [49–51].…”