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ChromID identifies the protein interactome at chromatin marks

ABSTRACT: Chromatin modifications regulate genome function by recruiting protein factors to the genome. However, the protein composition at distinct chromatin modifications has yet to be fully characterized. In this study, we used natural protein domains as modular building blocks to develop engineered chromatin readers (eCRs) selective for DNA methylation and histone trimethylation at H3K4, H3K9 and H3K27 residues. We first demonstrated their utility as selective chromatin binders in living cells by stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localization, genomic distribution and histone-modification-binding preference. By fusing eCRs to the biotin ligase BASU, we established ChromID, a method for identifying the chromatin-dependent protein interactome on the basis of proximity biotinylation, and applied it to distinct chromatin modifications in mouse stem cells. Using a synthetic dual-modification reader, we also uncovered the protein composition at bivalently modified promoters marked by H3K4me3 and H3K27me3. These results highlight the ability of ChromID to obtain a detailed view of protein interaction networks on chromatin.

ORGANISM(S): Mus musculus

PROVIDER: GSE128907 | GEO | 2020/02/21

REPOSITORIES: GEO

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ChromID reveals the proteome composition of key chromatin states in murine stem cells

Project description:Chromatin modifications instruct genome function through spatiotemporal recruitment of regulatory factors to the genome. However, how these modifications define the proteome composition at distinct chromatin states remains to be fully characterized. Here, we made use of natural protein domains as modular building blocks to develop engineered chromatin readers (eCRs) selective for histone and DNA modifications. By stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localisation, genomicdistribution and histone-PTM-binding preference, we first demonstrate their applicability as selective chromatin binders in living cells. Finally, we exploit the binding specificity of eCRs to establish ChromID, a new method for chromatin-dependent proteome identification based on proximity biotinylation. We use ChromID to reveal the proteome at distinct chromatin states in mouse stem cells, and by using a synthetic dual-modification reader, we furthermore uncover the protein composition at bivalent promoters marked by H3K4me3 and H3K27me3. These results highlight the applicability of ChromID as novel method to obtaina detailed view of the protein interaction network determined by the chemical language on chromatin.

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