Dataset Information

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

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Stem Cell, Cell Culture

SUBMITTER: Tuncay Baubec

LAB HEAD: Tuncay Baubec

PROVIDER: PXD014483 | Pride | 2020-04-30

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20181113_002_S187814_RPX40_Taf3_2xPHD_13XL_BASU_2_Taf3_13XL_BASU.raw	Raw
	20181113_003_S187817_RPX40_Cbx1_2xChromo_13XL_BASU_1_Cbx1_13XL_BASU.raw	Raw
	20181113_004_S187809_RPX40_13XL_BASU_1_13XL_BASU.raw	Raw
	20181113_005_S187825_RPX40_Cbx7_Chromo_Taf3_PHD_13XL_BASU_1_Cbx7_Taf3_13XL_BASU.raw	Raw
	20181113_006_S187821_RPX40_Cbx7_2xChromo_13XL_BASU_4_Cbx7_13XL_BASU.raw	Raw

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Publications

ChromID identifies the protein interactome at chromatin marks.

Villaseñor Rodrigo R Pfaendler Ramon R Ambrosi Christina C Butz Stefan S Giuliani Sara S Bryan Elana E Sheahan Thomas W TW Gable Annika L AL Schmolka Nina N Manzo Massimiliano M Wirz Joël J Feller Christian C von Mering Christian C Aebersold Ruedi R Voigt Philipp P Baubec Tuncay T

Nature biotechnology 20200302 6

Chromatin modifications regulate genome function by recruiting proteins 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 tri-methylation at H3K4, H3K9 and H3K27 residues. We first demonstrated their utility as selective chromatin binders in living cells by stably exp ...[more]

PMID: 32123383

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