Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells

Mol Cell. 2016 Jun 16;62(6):848-861. doi: 10.1016/j.molcel.2016.04.025. Epub 2016 May 26.

Abstract

Global demethylation is part of a conserved program of epigenetic reprogramming to naive pluripotency. The transition from primed hypermethylated embryonic stem cells (ESCs) to naive hypomethylated ones (serum-to-2i) is a valuable model system for epigenetic reprogramming. We present a mathematical model, which accurately predicts global DNA demethylation kinetics. Experimentally, we show that the main drivers of global demethylation are neither active mechanisms (Aicda, Tdg, and Tet1-3) nor the reduction of de novo methylation. UHRF1 protein, the essential targeting factor for DNMT1, is reduced upon transition to 2i, and so is recruitment of the maintenance methylation machinery to replication foci. Concurrently, there is global loss of H3K9me2, which is needed for chromatin binding of UHRF1. These mechanisms synergistically enforce global DNA hypomethylation in a replication-coupled fashion. Our observations establish the molecular mechanism for global demethylation in naive ESCs, which has key parallels with those operating in primordial germ cells and early embryos.

MeSH terms

  • 5-Methylcytosine / analogs & derivatives
  • 5-Methylcytosine / metabolism
  • Animals
  • CCAAT-Enhancer-Binding Proteins
  • Cells, Cultured
  • Cellular Reprogramming*
  • DNA Methylation*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Embryonic Stem Cells / metabolism*
  • Epigenesis, Genetic*
  • Gene Expression Regulation, Developmental*
  • Histones / metabolism
  • Mice
  • Models, Genetic
  • Mutation
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Proto-Oncogene Proteins / genetics
  • Proto-Oncogene Proteins / metabolism
  • Time Factors
  • Transfection
  • Ubiquitin-Protein Ligases

Substances

  • CCAAT-Enhancer-Binding Proteins
  • DNA-Binding Proteins
  • Histones
  • Nuclear Proteins
  • Proto-Oncogene Proteins
  • TET1 protein, mouse
  • Tet2 protein, mouse
  • 5-hydroxymethylcytosine
  • 5-Methylcytosine
  • Ubiquitin-Protein Ligases
  • Uhrf1 protein, mouse