Abstract
Histone post-translational modifications (PTMs) and their recognition by histone readers exert crucial functions in eukaryotes. Despite extensive studies, conservation and diversity of histone PTM regulation between animals and plants remain less explored because of a lack of systematic knowledge of histone readers in plants. Based on a high-throughput surface plasmon resonance imaging (SPRi) platform, we report the lab-on-chip profiling of interactions between 204 putative reader domains and 11 types of histone peptides in Arabidopsis thaliana. Eleven reader hits were then chosen for histone combinatorial readout pattern profiling. Systematic analysis of histone PTM recognition in Arabidopsis thaliana reveals that plant and human histone readers share conservation in domain types and recognition mechanisms. The differences in particular histone mark recognition by transcription regulator EML1 and DNA damage repair factor MSH6 indicate plant-specific histone PTMs function in Arabidopsis thaliana acquired during evolution.
Highlights
Histone post-translational modifications (PTMs) constitute important epigenetic regulation mechanisms in eukaryotes
We identified several unique histone ‘‘mark-reader’’ pairs in Arabidopsis thaliana, including the single Tudor domain protein EML1 that recognizes H3K4me3, and the DNA damage repair protein MSH6 that recognizes H3K4me3
WD40 repeats domain and Ankyrin repeats domain proteins were not chosen because many proteins in these families are cytoplasmic, and only a few members of both families have been reported to be histone readers in humans
Summary
Histone post-translational modifications (PTMs) constitute important epigenetic regulation mechanisms in eukaryotes. Histones can be covalently modified with various chemical groups, such as methyl, acetyl, and phosphor groups. These histone PTM marks regulate chromatin states and transcription through a trans- or cis-mechanism. The Bromo, double PHD finger (DPF), and YEATS domains recognize histone acylation modification in mammals (Dhalluin et al, 1999; Li et al, 2014, 2016; Wan et al, 2017; Zeng et al, 2010; Zhao et al, 2016, 2017a). Recognition of histone modifications by histone readers has type, site, and state (e.g., mono-, di-, and tri-methylation of lysine) specificity, ensuring epigenetic regulation complexity
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