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Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components.
Nucleic Acids Res. 51, 2671-2690 (2023)
The establishment of cellular identity is driven by transcriptional and epigenetic regulators of the chromatin proteome - the chromatome. Comprehensive analyses of the chromatome composition and dynamics can therefore greatly improve our understanding of gene regulatory mechanisms. Here, we developed an accurate mass spectrometry (MS)-based proteomic method called Chromatin Aggregation Capture (ChAC) followed by Data-Independent Acquisition (DIA) and analyzed chromatome reorganizations during major phases of pluripotency. This enabled us to generate a comprehensive atlas of proteomes, chromatomes, and chromatin affinities for the ground, formative and primed pluripotency states, and to pinpoint the specific binding and rearrangement of regulatory components. These comprehensive datasets combined with extensive analyses identified phase-specific factors like QSER1 and JADE1/2/3 and provide a detailed foundation for an in-depth understanding of mechanisms that govern the phased progression of pluripotency. The technical advances reported here can be readily applied to other models in development and disease.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Data-independent Acquisition; Stem-cell Transition; Naive Pluripotency; Profiling Reveals; Mouse Epiblast; Proteins; State; Hbo1; Progression; Enrichment
ISSN (print) / ISBN
0305-1048
e-ISSN
1362-4962
Journal
Nucleic Acids Research
Quellenangaben
Volume: 51,
Issue: 6,
Pages: 2671-2690
Publisher
Oxford University Press
Publishing Place
Great Clarendon St, Oxford Ox2 6dp, England
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Stem Cell Research (ISF)
Grants
Deutsche Forschungsgemeinschaft (DFG, German Research foundation)