PXD007154 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Integrative proteomics reveals a protective role of PRC2 for the ground state pluripotent epigenome |
Description | The ground state of pluripotency is defined as a basal proliferative state free of epigenetic restriction, represented by mouse embryonic stem cells (ESCs) cultured with two kinase inhibitors (so-called ā2iā). Through comparison with serum-grown ESCs, we identify epigenetic features characterizing 2i ESCs by proteome profiling of chromatin including post-translational histone modifications. The most prominent difference is H3K27me3 and its enzymatic writer complex PRC2 that are highly abundant on eu- and heterochromatin in 2i ESCs, with H3K27me3 redistributing outside canonical PRC2 targets in a CpG-dependent fashion. Using PRC2-deficient 2i ESCs, we identify epigenetic crosstalk with H3K27me3, including significant increases in H4 acetylation and DNA methylation. This suggests that the unique H3K27me3 configuration protects 2i ESCs from preparation to lineage priming. Interestingly, removal of DNA methylation in PRC2-deficient 2i ESCs lacking H3K27me3 using 5-azacytidine hardly affected ESC viability and transcriptome, showing that ESCs are independent of both major repressive epigenetic marks. |
HostingRepository | PRIDE |
AnnounceDate | 2018-11-21 |
AnnouncementXML | Submission_2018-11-21_07:09:55.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Guido van Mierlo |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | N6-carbamoyl-L-lysine; monomethylated residue; phosphorylated residue; N6-crotonyl-L-lysine; N6: N6; formylated residue; monohydroxylated residue; acetylated residue; dimethylated residue |
Instrument | Orbitrap Fusion; Q Exactive; Synapt MS |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2017-07-31 01:40:44 | ID requested | |
⏵ 1 | 2018-11-21 07:09:56 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
curator keyword: Biological |
submitter keyword: Chromatin profiling, mouse embryonic stem cells, pluripotency, histone modifications, PRC2 |
Contact List
Hendrik Marks |
contact affiliation | Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, the Netherlands |
contact email | H.Marks@ncmls.ru.nl |
lab head | |
Guido van Mierlo |
contact affiliation | Radboud University |
contact email | guidovanmierlo@gmail.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD007154
- Label: PRIDE project
- Name: Integrative proteomics reveals a protective role of PRC2 for the ground state pluripotent epigenome