Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate

Cell Stem Cell. 2018 Nov 1;23(5):727-741.e9. doi: 10.1016/j.stem.2018.08.016. Epub 2018 Sep 13.

Abstract

Here, we report DNA methylation and hydroxymethylation dynamics at nucleotide resolution using C/EBPα-enhanced reprogramming of B cells into induced pluripotent cells (iPSCs). We observed successive waves of hydroxymethylation at enhancers, concomitant with a decrease in DNA methylation, suggesting active demethylation. Consistent with this finding, ablation of the DNA demethylase Tet2 almost completely abolishes reprogramming. C/EBPα, Klf4, and Tfcp2l1 each interact with Tet2 and recruit the enzyme to specific DNA sites. During reprogramming, some of these sites maintain high levels of 5hmC, and enhancers and promoters of key pluripotency factors become demethylated as early as 1 day after Yamanaka factor induction. Surprisingly, methylation changes precede chromatin opening in distinct chromatin regions, including Klf4 bound sites, revealing a pioneer factor activity associated with alternation in DNA methylation. Rapid changes in hydroxymethylation similar to those in B cells were also observed during compound-accelerated reprogramming of fibroblasts into iPSCs, highlighting the generality of our observations.

Keywords: DNA hydroxymethylation; DNA methylation; Tet enzymes; active demethylation; cell fate decisions; cell reprogramming; epigenetics; iPSCs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cells, Cultured
  • Cellular Reprogramming / genetics*
  • DNA Methylation*
  • DNA-Binding Proteins / genetics*
  • DNA-Binding Proteins / metabolism*
  • Enhancer Elements, Genetic / genetics*
  • Female
  • Fibroblasts / cytology
  • Fibroblasts / metabolism
  • Induced Pluripotent Stem Cells / cytology*
  • Induced Pluripotent Stem Cells / metabolism
  • Male
  • Mice
  • Mice, Knockout
  • Proto-Oncogene Proteins / genetics*
  • Proto-Oncogene Proteins / metabolism*
  • Transcription Factors / metabolism*

Substances

  • DNA-Binding Proteins
  • Proto-Oncogene Proteins
  • Transcription Factors
  • Tet2 protein, mouse