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

Citation

Shu, J., Chen, C., Thapa, R.K., Bian, S., Nguyen, V., Yu, K., Yuan, Z.C., Liu, J., Kohalmi, S.E., Li, C., Cui, Y. (2019). Genome-wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings. Plant Direct, [online] 3(1), http://dx.doi.org/10.1002/pld3.100

Plain language summary

The Polycomb Group (PcG) proteins are key epigenetic regulators in eukaryotes. In Arabidopsis, CURLY LEAF (CLF) and SWINGER (SWN) are two major core components of PcG, playing vital roles in many plant growth and development processes. For instance, CLF is known to be necessary for the control of leaf and flower morphology as well as maintaining root meristem activity. The clf mutants display severe phenotypes including dwarfism, curly leaf, and early flowering. The swn mutants show weak changes during vegetative phase transition. However, the clf swn double mutants lose the capacity to differentiate and form massive somatic embryo-like structures.

Despite their importance, genome-wide profiles of CLF and SWN have not yet been determined and compared. In this study, we generated transgenic lines to profile the genome-wide distributions of CLF and SWN in Arabidopsis seedlings. Here, we generated Arabidopsis transgenic lines expressing tagged CLF or SWN. We also profiled the genome-wide changes of the transcriptomes in the clf, swn, and clf swn mutants. These genomics data would greatly facilitate the deciphering of the detailed roles of plant PcG proteins in various growth and developmental processes. Thus this work provides a useful resource for the plant epigenetics community for dissecting the functions of PRC2 in plant growth and development.

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 Arabidopsis (Arabidopsis thaliana), 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 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 PRC2 in plant growth and development.