PXD007154

PXD007154 is an original dataset announced via ProteomeXchange.

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 “2i”). 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

Revision	Datetime	Status	ChangeLog Entry
0	2017-07-31 01:40:44	ID requested
⏵ 1	2018-11-21 07:09:56	announced

Dataset with its publication pending

curator keyword: Biological

submitter keyword: Chromatin profiling, mouse embryonic stem cells, pluripotency, histone modifications, PRC2

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

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PRIDE project URI

• PRIDE
  1. PXD007154
     1. Label: PRIDE project
     2. Name: Integrative proteomics reveals a protective role of PRC2 for the ground state pluripotent epigenome