DNA Methylome Analysis Identifies Transcription Factor-Based Epigenomic Signatures of Multilineage Competence in Neural Stem/Progenitor Cells

Cell Rep. 2017 Sep 19;20(12):2992-3003. doi: 10.1016/j.celrep.2017.08.086.


Regulation of the epigenome during in vivo specification of brain stem cells is still poorly understood. Here, we report DNA methylome analyses of directly sampled cortical neural stem and progenitor cells (NS/PCs) at different development stages, as well as those of terminally differentiated cortical neurons, astrocytes, and oligodendrocytes. We found that sequential specification of cortical NS/PCs is regulated by two successive waves of demethylation at early and late development stages, which are responsible for the establishment of neuron- and glia-specific low-methylated regions (LMRs), respectively. The regulatory role of demethylation of the gliogenic genes was substantiated by the enrichment of nuclear factor I (NFI)-binding sites. We provide evidence that de novo DNA methylation of neuron-specific LMRs establishes glia-specific epigenotypes, essentially by silencing neuronal genes. Our data highlight the in vivo implications of DNA methylation dynamics in shaping epigenomic features that confer the differentiation potential of NS/PCs sequentially during development.

Keywords: DNA methylation; NFI; differentiation; epigenetics; neural stem/progenitor cell; nuclear factor I.

MeSH terms

  • Amino Acid Motifs
  • Animals
  • Base Sequence
  • Binding Sites
  • Cell Lineage / genetics*
  • DNA Demethylation
  • DNA Methylation / genetics*
  • Epigenomics*
  • Gene Expression Regulation
  • Mice, Transgenic
  • NFI Transcription Factors / chemistry
  • NFI Transcription Factors / metabolism
  • Neural Stem Cells / cytology*
  • Neural Stem Cells / metabolism*
  • Neuroglia / metabolism
  • Phenotype
  • Promoter Regions, Genetic / genetics
  • Protein Binding
  • Transcription Factors / metabolism*


  • NFI Transcription Factors
  • Transcription Factors