PXD013067

PXD013067 is an original dataset announced via ProteomeXchange.

Title	Untargeted histone profiling of human embryonic stem cell conversion over time reveals fundamental epigenetic changes between pluripotent and naive states
Description	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.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_10:24:58.512.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD013067
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Maarten Dhaenens
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Methyl; Succinyl; Butyryl; Oxidation; Dimethyl; Acetyl
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2019-03-12 09:09:04	ID requested
⏵ 1	2024-10-07 10:24:59	announced

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]

curator keyword: Biological

submitter keyword: human embryonic stem cells

pluripotency

naïve

epigenetics

histone modification

mass spectrometry

Maarten Dhaenens
contact affiliation	University Ghent
contact email	maarten.dhaenens@ugent.be
lab head
Maarten Dhaenens
contact affiliation	Faculity of Pharmaceutical Biotechnology
contact email	maarten.dhaenens@ugent.be
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/11/PXD013067

PRIDE project URI

• PRIDE
  1. PXD013067
     1. Label: PRIDE project
     2. Name: Untargeted histone profiling of human embryonic stem cell conversion over time reveals fundamental epigenetic changes between pluripotent and naive states