Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons

Elife. 2019 Jan 15;8:e40197. doi: 10.7554/eLife.40197.

Abstract

Direct reprogramming of fibroblasts to neurons induces widespread cellular and transcriptional reconfiguration. Here, we characterized global epigenomic changes during the direct reprogramming of mouse fibroblasts to neurons using whole-genome base-resolution DNA methylation (mC) sequencing. We found that the pioneer transcription factor Ascl1 alone is sufficient for inducing the uniquely neuronal feature of non-CG methylation (mCH), but co-expression of Brn2 and Mytl1 was required to establish a global mCH pattern reminiscent of mature cortical neurons. Ascl1 alone induced promoter CG methylation (mCG) of fibroblast specific genes, while BAM overexpression additionally targets a competing myogenic program and directs a more faithful conversion to neuronal cells. Ascl1 induces local demethylation at its binding sites. Surprisingly, co-expression with Brn2 and Mytl1 inhibited the ability of Ascl1 to induce demethylation, suggesting a contextual regulation of transcription factor - epigenome interaction. Finally, we found that de novo methylation by DNMT3A is required for efficient neuronal reprogramming.

Keywords: DNA methylation; epigenetics; epigenomics; genetics; genomics; mouse; neuron; regenerative medicine; reprogramming; stem cells; transdifferentiation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cellular Reprogramming / genetics*
  • DNA (Cytosine-5-)-Methyltransferases / metabolism
  • DNA Methylation / genetics*
  • Down-Regulation / genetics
  • Fibroblasts / cytology*
  • Gene Expression Regulation, Developmental
  • Gene Silencing
  • Mice, Inbred C57BL
  • Neurons / cytology*
  • Promoter Regions, Genetic
  • Transcription Factors / metabolism
  • Transcription, Genetic

Substances

  • Transcription Factors
  • DNA (Cytosine-5-)-Methyltransferases
  • DNA methyltransferase 3A