FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency

Cell Stem Cell. 2013 Sep 5;13(3):351-9. doi: 10.1016/j.stem.2013.06.004. Epub 2013 Jul 11.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • DNA (Cytosine-5-)-Methyltransferases / genetics
  • DNA (Cytosine-5-)-Methyltransferases / metabolism*
  • DNA Methylation* / drug effects
  • DNA Methyltransferase 3B
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Embryonic Stem Cells / drug effects
  • Embryonic Stem Cells / physiology*
  • Epigenetic Repression
  • Epigenomics
  • Fibroblast Growth Factors / metabolism
  • Genome / genetics
  • Germ Cells / physiology
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / metabolism
  • MAP Kinase Signaling System / drug effects
  • Mice
  • Nanog Homeobox Protein
  • Pluripotent Stem Cells / drug effects
  • Pluripotent Stem Cells / physiology*
  • Protein Binding
  • Protein Kinase Inhibitors / pharmacology
  • Proto-Oncogene Proteins / genetics
  • Proto-Oncogene Proteins / metabolism*
  • RNA-Binding Proteins
  • Regulatory Sequences, Nucleic Acid / genetics
  • Transcription Factors / genetics
  • Transcription Factors / metabolism

Substances

  • DNA-Binding Proteins
  • Homeodomain Proteins
  • Nanog Homeobox Protein
  • Nanog protein, mouse
  • Prdm14 protein, mouse
  • Protein Kinase Inhibitors
  • Proto-Oncogene Proteins
  • RNA-Binding Proteins
  • TET1 protein, mouse
  • Transcription Factors
  • Fibroblast Growth Factors
  • DNA (Cytosine-5-)-Methyltransferases

Associated data

  • GEO/GSE42923