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PXD017235 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleChromID identifies the protein interactome at chromatin marks
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, genomic distribution 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 obtain a detailed view of the protein interaction network determined by the chemical language on chromatin.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterChristian Feller
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListmonomethylated residue; phosphorylated residue; acetylated residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-01-21 06:13:18ID requested
12020-04-29 22:03:00announced
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
Ruedi Aebersold
contact affiliationDepartment of Biology, Institute of Molecular Systems Biology, ETH Zürich
contact emailaebersold@imsb.biol.ethz.ch
lab head
Christian Feller
contact affiliationETH Zurich
contact emailfeller.christian@gmail.com
dataset submitter
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Dataset FTP location
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