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PXD013067

PXD013067 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleUntargeted histone profiling of human embryonic stem cell conversion over time reveals fundamental epigenetic changes between pluripotent and naive states
DescriptionRecently, 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-07
AnnouncementXMLSubmission_2024-10-07_10:24:58.512.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD013067
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterMaarten Dhaenens
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListMethyl; Succinyl; Butyryl; Oxidation; Dimethyl; Acetyl
InstrumentTripleTOF 5600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-03-12 09:09:04ID requested
12024-10-07 10:24:59announced
Publication List
10.6019/PXD013067;
10.1038/s41598-019-53681-6;
De Clerck L, Taelman J, Popovic M, Willems S, Van der Jeught M, Heindryckx B, De Sutter P, Marks H, Deforce D, Dhaenens M, Untargeted histone profiling during naive conversion uncovers conserved modification markers between mouse and human. Sci Rep, 9(1):17240(2019) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: human embryonic stem cells
pluripotency
naïve
epigenetics
histone modification
mass spectrometry
Contact List
Maarten Dhaenens
contact affiliationUniversity Ghent
contact emailmaarten.dhaenens@ugent.be
lab head
Maarten Dhaenens
contact affiliationFaculity of Pharmaceutical Biotechnology
contact emailmaarten.dhaenens@ugent.be
dataset submitter
Full Dataset Link List
Dataset FTP location
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