title: Stable methylation at promoters distinguishes epiblast stem cells from embryonic stem cells and the in vivo epiblasts.
abstract: Embryonic Stem Cells (ESCs) and Epiblast Stem Cells (EpiSCs) are the in vitro representatives of naïve and primed pluripotency, respectively. It is currently unclear how their epigenomes underpin the phenotypic and molecular characteristics of these distinct pluripotent states. Here, we performed a genome-wide comparison of DNA methylation between ESCs and EpiSCs by MethylCap-Seq. We observe that promoters are preferential targets for methylation in EpiSC compared to ESCs, in particular high CpG island promoters. This is in line with upregulation of the de novo methyltransferases Dnmt3a1 and Dnmt3b in EpiSC, and downregulation of the demethylases Tet1 and Tet2. Remarkably, the observed DNA methylation signature is specific to EpiSCs and differs from that of their in vivo counterpart, the postimplantation epiblast. Using a subset of promoters that are differentially methylated, we show that DNA methylation is established within a few days during in vitro outgrowth of the epiblast, and also occurs when ESCs are converted to EpiSCs in vitro. Once established, this methylation is stable, as ES-like cells obtained by in vitro reversion of EpiSCs display an epigenetic memory that only extensive passaging and sub-cloning are able to almost completely erase.
authors.affiliation: 1 INRA , UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France .
authors.forename: Anne-Clémence
authors.initials: AC
authors.lastname: Veillard
authors.forename: Hendrik
authors.initials: H
authors.lastname: Marks
authors.forename: Andreia Sofia
authors.initials: AS
authors.lastname: Bernardo
authors.forename: Luc
authors.initials: L
authors.lastname: Jouneau
authors.forename: Denis
authors.initials: D
authors.lastname: Laloë
authors.forename: Laurent
authors.initials: L
authors.lastname: Boulanger
authors.forename: Anita
authors.initials: A
authors.lastname: Kaan
authors.forename: Vincent
authors.initials: V
authors.lastname: Brochard
authors.forename: Matteo
authors.initials: M
authors.lastname: Tosolini
authors.forename: Roger
authors.initials: R
authors.lastname: Pedersen
authors.forename: Henk
authors.initials: H
authors.lastname: Stunnenberg
authors.forename: Alice
authors.initials: A
authors.lastname: Jouneau
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D019175:DNA Methylation; D053595:Embryonic Stem Cells / Q000378:metabolism*; D044127:Epigenesis, Genetic; D005260:Female; D015870:Gene Expression; D018507:Gene Expression Regulation, Developmental; D005855:Germ Layers / Q000166:cytology*; D008297:Male; D008810:Mice, Inbred C57BL; D058977:Molecular Sequence Annotation; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA
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