MeCP2 regulates gene expression through recognition of H3K27me3

Wooje Lee,Jung-Mi Yun,Takbum Ohn,Qizhi Gong,Jeeho Kim

doi:10.1038/s41467-020-16907-0

Abstract

MeCP2 plays a multifaceted role in gene expression regulation and chromatin organization. Interaction between MeCP2 and methylated DNA in the regulation of gene expression is well established. However, the widespread distribution of MeCP2 suggests it has additional interactions with chromatin. Here we demonstrate, by both biochemical and genomic analyses, that MeCP2 directly interacts with nucleosomes and its genomic distribution correlates with that of H3K27me3. In particular, the methyl-CpG-binding domain of MeCP2 shows preferential interactions with H3K27me3. We further observe that the impact of MeCP2 on transcriptional changes correlates with histone post-translational modification patterns. Our findings indicate that MeCP2 interacts with genomic loci via binding to DNA as well as histones, and that interaction between MeCP2 and histone proteins plays a key role in gene expression regulation.

Highlights

Methyl CpG binding protein 2 (MeCP2) plays a multifaceted role in gene expression regulation and chromatin organization
To test whether MeCP2 is associated with other histone subunits, the co-IPed proteins from Benzonase treated nuclear extracts were examined for the presence of H3 and H4 by western blotting
MeCP2, H3K27me[3], and H3K9ac were abundant (Fig. 6h); while DNA is hypomethylated (Fig. 6g). These results demonstrate that MeCP2 binding to gene expression regulatory regions is independent of DNA methylation but correlated with both H3K27me[3] and H3K9ac

Summary

Results

MeCP2 is associated with nucleosomes in vivo. MeCP2 interacts with several nuclear proteins including DNMT1, CoREST, Suv39H1, and c-SKI20–22. When nucleosomes were unstable (group[3], n = 33,644), MeCP2 enrichment showed a strong correlation with H3K27me[3] while H3K9ac levels are high (Fig. 2d) These results indicate that MeCP2 binding is correlated with H3K27me[3]. Interactions between bait proteins (purified GST, GST-tagged MeCP2 or MBD) and prey proteins (recombinant mononucleosomes, either containing unmodified H3 or H3K27me3) were evaluated by pulldown analysis with glutathione affinity column (Fig. 3d and Supplementary Fig. 5A). Both full length MeCP2 and a MeCP2-absent mononucleosome loci.

H3K27me3 8

20 Methyl CA of CHH

Discussion

Methods