Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis

Life Sci Alliance. 2019 Feb 27;2(2):e201900331. doi: 10.26508/lsa.201900331. Print 2019 Apr.


Dynamic changes in DNA (hydroxy-)methylation are fundamental for stem cell differentiation. However, the signature of these epigenetic marks in specific cell types during corticogenesis is unknown. Moreover, site-specific manipulation of cytosine modifications is needed to reveal the significance and function of these changes. Here, we report the first assessment of (hydroxy-)methylation in neural stem cells, neurogenic progenitors, and newborn neurons during mammalian corticogenesis. We found that gain in hydroxymethylation and loss in methylation occur sequentially at specific cellular transitions during neurogenic commitment. We also found that these changes predominantly occur within enhancers of neurogenic genes up-regulated during neurogenesis and target of pioneer transcription factors. We further optimized the use of dCas9-Tet1 manipulation of (hydroxy-)methylation, locus-specifically, in vivo, showing the biological relevance of our observations for Dchs1, a regulator of corticogenesis involved in developmental malformations and cognitive impairment. Together, our data reveal the dynamics of cytosine modifications in lineage-related cell types, whereby methylation is reduced and hydroxymethylation gained during the neurogenic lineage concurrently with up-regulation of pioneer transcription factors and activation of enhancers for neurogenic genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5-Methylcytosine / analogs & derivatives*
  • 5-Methylcytosine / physiology
  • Animals
  • CRISPR-Associated Protein 9 / metabolism
  • Cadherins / metabolism
  • Cell Differentiation
  • Cell Lineage / physiology
  • Cytosine / metabolism
  • DNA Methylation / genetics*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Embryonic Stem Cells / metabolism
  • Epigenesis, Genetic / genetics
  • Female
  • Gene Expression Regulation, Developmental / genetics
  • Mice
  • Mice, Inbred C57BL
  • Neural Stem Cells / metabolism*
  • Neurogenesis / genetics*
  • Oncogene Proteins, Fusion / metabolism
  • Pregnancy
  • Proto-Oncogene Proteins / genetics
  • Proto-Oncogene Proteins / metabolism
  • Transcription Factors
  • Transcriptome


  • Cadherins
  • DNA-Binding Proteins
  • Dchs1 protein, mouse
  • Oncogene Proteins, Fusion
  • Proto-Oncogene Proteins
  • TET1 protein, mouse
  • Transcription Factors
  • 5-hydroxymethylcytosine
  • 5-Methylcytosine
  • Cytosine
  • CRISPR-Associated Protein 9