Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components
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Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components. / Ugur, Enes; de la Porte, Alexandra; Qin, Weihua; Bultmann, Sebastian; Ivanova, Alina; Drukker, Micha; Mann, Matthias; Wierer, Michael; Leonhardt, Heinrich.
In: Nucleic Acids Research, Vol. 51, No. 6, 2023, p. 2671-2690.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components
AU - Ugur, Enes
AU - de la Porte, Alexandra
AU - Qin, Weihua
AU - Bultmann, Sebastian
AU - Ivanova, Alina
AU - Drukker, Micha
AU - Mann, Matthias
AU - Wierer, Michael
AU - Leonhardt, Heinrich
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
KW - DATA-INDEPENDENT ACQUISITION
KW - STEM-CELL TRANSITION
KW - NAIVE PLURIPOTENCY
KW - PROFILING REVEALS
KW - MOUSE EPIBLAST
KW - PROTEINS
KW - STATE
KW - HBO1
KW - PROGRESSION
KW - ENRICHMENT
U2 - 10.1093/nar/gkad058
DO - 10.1093/nar/gkad058
M3 - Journal article
C2 - 36806742
VL - 51
SP - 2671
EP - 2690
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 6
ER -
ID: 339139754