title: FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency.
abstract: Genome-wide erasure of DNA methylation takes place in primordial germ cells (PGCs) and early embryos and is linked with pluripotency. Inhibition of Erk1/2 and Gsk3β signaling in mouse embryonic stem cells (ESCs) by small-molecule inhibitors (called 2i) has recently been shown to induce hypomethylation. We show by whole-genome bisulphite sequencing that 2i induces rapid and genome-wide demethylation on a scale and pattern similar to that in migratory PGCs and early embryos. Major satellites, intracisternal A particles (IAPs), and imprinted genes remain relatively resistant to erasure. Demethylation involves oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), impaired maintenance of 5mC and 5hmC, and repression of the de novo methyltransferases (Dnmt3a and Dnmt3b) and Dnmt3L. We identify a Prdm14- and Nanog-binding cis-acting regulatory region in Dnmt3b that is highly responsive to signaling. These insights provide a framework for understanding how signaling pathways regulate reprogramming to an epigenetic ground state of pluripotency.
authors.affiliation: Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK. gabriella.ficz@babraham.ac.uk
authors.forename: Gabriella
authors.initials: G
authors.lastname: Ficz
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Hore
authors.forename: Fátima
authors.initials: F
authors.lastname: Santos
authors.forename: Heather J
authors.initials: HJ
authors.lastname: Lee
authors.forename: Wendy
authors.initials: W
authors.lastname: Dean
authors.forename: Julia
authors.initials: J
authors.lastname: Arand
authors.forename: Felix
authors.initials: F
authors.lastname: Krueger
authors.forename: David
authors.initials: D
authors.lastname: Oxley
authors.forename: Yu-Lee
authors.initials: YL
authors.lastname: Paul
authors.forename: Jörn
authors.initials: J
authors.lastname: Walter
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Cook
authors.forename: Simon
authors.initials: S
authors.lastname: Andrews
authors.forename: Miguel R
authors.initials: MR
authors.lastname: Branco
authors.forename: Wolf
authors.initials: W
authors.lastname: Reik
mesh_terms: D000818:Animals; D002460:Cell Line; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation / Q000187:drug effects; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D053595:Embryonic Stem Cells / Q000187:drug effects / Q000502:physiology*; D063185:Epigenetic Repression; D057890:Epigenomics; D005346:Fibroblast Growth Factors / Q000378:metabolism; D016678:Genome / Q000235:genetics; D005854:Germ Cells / Q000502:physiology; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D020935:MAP Kinase Signaling System / Q000187:drug effects; D051379:Mice; D000071317:Nanog Homeobox Protein; D039904:Pluripotent Stem Cells / Q000187:drug effects / Q000502:physiology*; D011485:Protein Binding; D047428:Protein Kinase Inhibitors / Q000494:pharmacology; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D000097584:DNA Methyltransferase 3B
chemical_list: D004248:DNA (Cytosine-5-)-Methyltransferases; D004268:DNA-Binding Proteins; D005346:Fibroblast Growth Factors; D018398:Homeodomain Proteins; D000071317:Nanog Homeobox Protein; D047428:Protein Kinase Inhibitors; D011518:Proto-Oncogene Proteins; D016601:RNA-Binding Proteins; D014157:Transcription Factors; D000097584:DNA Methyltransferase 3B; C475540:Nanog protein, mouse; C531066:Prdm14 protein, mouse; C540839:TET1 protein, mouse