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.
Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Animals
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Cell Line
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DNA (Cytosine-5-)-Methyltransferases / genetics
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DNA (Cytosine-5-)-Methyltransferases / metabolism*
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DNA Methylation* / drug effects
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DNA Methyltransferase 3B
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DNA-Binding Proteins / genetics
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DNA-Binding Proteins / metabolism*
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Embryonic Stem Cells / drug effects
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Embryonic Stem Cells / physiology*
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Epigenetic Repression
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Epigenomics
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Fibroblast Growth Factors / metabolism
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Genome / genetics
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Germ Cells / physiology
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Homeodomain Proteins / genetics
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Homeodomain Proteins / metabolism
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MAP Kinase Signaling System / drug effects
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Mice
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Nanog Homeobox Protein
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Pluripotent Stem Cells / drug effects
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Pluripotent Stem Cells / physiology*
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Protein Binding
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Protein Kinase Inhibitors / pharmacology
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Proto-Oncogene Proteins / genetics
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Proto-Oncogene Proteins / metabolism*
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RNA-Binding Proteins
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Regulatory Sequences, Nucleic Acid / genetics
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Transcription Factors / genetics
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Transcription Factors / metabolism
Substances
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DNA-Binding Proteins
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Homeodomain Proteins
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Nanog Homeobox Protein
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Nanog protein, mouse
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Prdm14 protein, mouse
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Protein Kinase Inhibitors
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Proto-Oncogene Proteins
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RNA-Binding Proteins
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TET1 protein, mouse
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Transcription Factors
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Fibroblast Growth Factors
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DNA (Cytosine-5-)-Methyltransferases