Proteomics

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Untargeted histone profiling of human embryonic stem cell conversion over time reveals fundamental epigenetic changes between pluripotent and naive states


ABSTRACT: Recently, various groups managed to isolate naïve human embryonic stem cell (hESC) state in vitro has come into acceptance. However, a thorough epigenetic characterization of this human ground state, defined as a state without any epigenetic restrictions, and how that compares to mouse is currently lacking. Also, the epigenomic remodeling required to obtain the ground state, and the important transient processes occurring during the remodeling, have remained elusive in human. Here, we address these issues by using an untargeted mass spectrometry-based (MS) approach to profile the histone epigenome in a time-resolved experimental design. Special care was given to defining the naïve hESC state that was reached over 12 passages (P12, 37 days) in feeder-free conditions in this study. We found that conversion is a multi-staged process with a prominent cellular disturbance after stimulation (P3), an increase in cell proliferation between P3 and P6 and a naïve cell state stabilizing between P9 and P12. In total, 20 different histone post-translational modifications (hPTMs) changed significantly over time from primed to naïve hESCs. Most notably, H3K27me3 is the most prominently increasing hPTM in naïve hESCs, in line with what we recently described in mouse. Essentially, we present a first roadmap of the changing human histone epigenome from primed to naïve state and emphasize that the overlap with mouse hints at a conserved Mammalian epigenetic signature of the ground state.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Early Embryonic Cell

SUBMITTER: Maarten Dhaenens  

LAB HEAD: Maarten Dhaenens

PROVIDER: PXD013067 | Pride | 2019-11-27

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
171006_LDC_hESC_Naive_P0_2.wiff Wiff
171006_LDC_hESC_Naive_P0_2.wiff.scan Wiff
171006_LDC_hESC_Naive_P0_2_B.wiff Wiff
171006_LDC_hESC_Naive_P0_2_B.wiff.scan Wiff
171006_LDC_hESC_Naive_P0_3.wiff Wiff
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Publications

Untargeted histone profiling during naive conversion uncovers conserved modification markers between mouse and human.

De Clerck Laura L   Taelman Jasin J   Popovic Mina M   Willems Sander S   Van der Jeught Margot M   Heindryckx Björn B   De Sutter Petra P   Marks Hendrik H   Deforce Dieter D   Dhaenens Maarten M  

Scientific reports 20191121 1


Recent progress has enabled the conversion of primed human embryonic stem cells (hESCs) to the naive state of pluripotency, resembling the well-characterized naive mouse ESCs (mESCs). However, a thorough histone epigenetic characterization of this conversion process is currently lacking, while its likeness to the mouse model has not been clearly established. Here, we profile the histone epigenome of hESCs during conversion in a time-resolved experimental design, using an untargeted mass spectrom  ...[more]

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