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PXD014483 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleChromID reveals the proteome composition of key chromatin states in murine stem cells
DescriptionChromatin 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterTuncay Baubec
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListmonohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-07-04 03:48:52ID requested
12020-04-29 22:02:41announced
Publication List
Villase, ñ, or R, Pfaendler R, Ambrosi C, Butz S, Giuliani S, Bryan E, Sheahan TW, Gable AL, Schmolka N, Manzo M, Wirz J, Feller C, von Mering C, Aebersold R, Voigt P, Baubec T, ChromID identifies the protein interactome at chromatin marks. Nat Biotechnol, 38(6):728-736(2020) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: Chromatin, Epigenetics, Synthetic Biology, Systems Biology, Chromatin Proteomics
Contact List
Tuncay Baubec
contact affiliationSNF Professor - Principal Investigator Systems Biology of Gene Regulation University of Zurich Campus Irchel Winterthurerstrasse 190 CH-8057 Zurich Switzerland
contact emailtuncay.baubec@uzh.ch
lab head
Tuncay Baubec
contact affiliationUniversity of Zurich
contact emailtuncay.baubec@uzh.ch
dataset submitter
Full Dataset Link List
Dataset FTP location
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