Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components
Nucleic Acids Research, vol. 51, pp. 2671–2690
Abstract
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.
Authors 9
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Max Planck Institute of Biochemistry · Ludwig-Maximilians-Universität München
Affiliation as printed
Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry , Martinsried 82152 , Germany
Faculty of Biology and Center for Molecular Biosystems (BioSysM) , Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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Affiliation as printed
Institute of Stem Cell Research , Helmholtz Center Munich, Neuherberg 85764, Germany
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Ludwig-Maximilians-Universität München
Affiliation as printed
Faculty of Biology and Center for Molecular Biosystems (BioSysM) , Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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Ludwig-Maximilians-Universität München
Affiliation as printed
Faculty of Biology and Center for Molecular Biosystems (BioSysM) , Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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Ludwig-Maximilians-Universität München
Affiliation as printed
Faculty of Biology and Center for Molecular Biosystems (BioSysM) , Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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Leiden University · Helmholtz Munich
Affiliation as printed
Division of Drug Discovery and Safety , Leiden Academic Centre for Drug Research (LACDR), Leiden University, Gorlaeus Building, 2333 CC RA Leiden, The Netherlands
Institute of Stem Cell Research , Helmholtz Center Munich, Neuherberg 85764, Germany
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Matthias Mann corresponding
University of Copenhagen · Novo Nordisk Foundation · Max Planck Institute of Biochemistry
Affiliation as printed
Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry , Martinsried 82152 , Germany
Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen , DK-2200 Copenhagen, Denmark
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Michael Wierer corresponding
University of Copenhagen · Max Planck Institute of Biochemistry
Affiliation as printed
Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry , Martinsried 82152 , Germany
Proteomics Research Infrastructure, University of Copenhagen , DK-2200 Copenhagen, Denmark
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Heinrich Leonhardt corresponding
Ludwig-Maximilians-Universität München
Affiliation as printed
Faculty of Biology and Center for Molecular Biosystems (BioSysM) , Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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