title: Synergistic mechanisms of DNA demethylation during transition to ground-state pluripotency.
abstract: Pluripotent stem cells (PSCs) occupy a spectrum of reversible molecular states ranging from a naive ground-state in 2i, to metastable embryonic stem cells (ESCs) in serum, to lineage-primed epiblast stem cells (EpiSCs). To investigate the role of DNA methylation (5mC) across distinct pluripotent states, we mapped genome-wide 5mC and 5-hydroxymethycytosine (5hmC) in multiple PSCs. Ground-state ESCs exhibit an altered distribution of 5mC and 5hmC at regulatory elements and dramatically lower absolute levels relative to ESCs in serum. By contrast, EpiSCs exhibit increased promoter 5mC coupled with reduced 5hmC, which contributes to their developmental restriction. Switch to 2i triggers rapid onset of both the ground-state gene expression program and global DNA demethylation. Mechanistically, repression of de novo methylases by PRDM14 drives DNA demethylation at slow kinetics, whereas TET1/TET2-mediated 5hmC conversion enhances both the rate and extent of hypomethylation. These processes thus act synergistically during transition to ground-state pluripotency to promote a robust hypomethylated state.
authors.affiliation: Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK ; Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK ; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK.
authors.forename: Jamie A
authors.initials: JA
authors.lastname: Hackett
authors.affiliation: Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK.
authors.forename: Sabine
authors.initials: S
authors.lastname: Dietmann
authors.affiliation: Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK ; Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK ; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK.
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Murakami
authors.affiliation: Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK.
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Down
authors.affiliation: Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK ; Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK.
authors.forename: Harry G
authors.initials: HG
authors.lastname: Leitch
authors.affiliation: Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK ; Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK ; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK.
authors.forename: M Azim
authors.initials: MA
authors.lastname: Surani
mesh_terms: D000818:Animals; D018929:Cell Culture Techniques; D002454:Cell Differentiation / Q000235:genetics*; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics; D049308:Dioxygenases; D053595:Embryonic Stem Cells; D005260:Female; D055786:Gene Knockout Techniques; D018392:Genomic Imprinting; D008297:Male; D051379:Mice; D039904:Pluripotent Stem Cells / Q000166:cytology*; D011518:Proto-Oncogene Proteins / Q000235:genetics
chemical_list: D004268:DNA-Binding Proteins; D011518:Proto-Oncogene Proteins; C540839:TET1 protein, mouse; D049308:Dioxygenases; C551914:Tet2 protein, mouse