Embryonic Stem Cell-Derived Neurons as a Model System for Epigenome Maturation during Development

Genes (Basel). 2023 Apr 22;14(5):957. doi: 10.3390/genes14050957.


DNA methylation in neurons is directly linked to neuronal genome regulation and maturation. Unlike other tissues, vertebrate neurons accumulate high levels of atypical DNA methylation in the CH sequence context (mCH) during early postnatal brain development. Here, we investigate to what extent neurons derived in vitro from both mouse and human pluripotent stem cells recapitulate in vivo DNA methylation patterns. While human ESC-derived neurons did not accumulate mCH in either 2D culture or 3D organoid models even after prolonged culture, cortical neurons derived from mouse ESCs acquired in vivo levels of mCH over a similar time period in both primary neuron cultures and in vivo development. mESC-derived neuron mCH deposition was coincident with a transient increase in Dnmt3a, preceded by the postmitotic marker Rbfox3 (NeuN), was enriched at the nuclear lamina, and negatively correlated with gene expression. We further found that methylation patterning subtly differed between in vitro mES-derived and in vivo neurons, suggesting the involvement of additional noncell autonomous processes. Our findings show that mouse ESC-derived neurons, in contrast to those of humans, can recapitulate the unique DNA methylation landscape of adult neurons in vitro over experimentally tractable timeframes, which allows their use as a model system to study epigenome maturation over development.

Keywords: DNA methylation; cell culture systems; epigenomics; neuronal maturation; neuroscience.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Brain
  • DNA Methylation / genetics
  • Embryonic Stem Cells / metabolism
  • Epigenome*
  • Humans
  • Mice
  • Neurons* / metabolism

Grants and funding

Monoclonal antibody generation and N.O. were funded by the Babraham Institute Knowledge Exchange and Commercialisation Fund. W.R. is funded by the BBSRC. E.W. was funded by the NHMRC APP1130168 and NHMRC APP1090116 project grants. R.L. was funded by Sylvia and Charles Viertel Senior Medical Research Fellowship, Howard Hughes Medical Institute International Research Scholarship, NHMRC GNT1178460 Investigator Grant and GNT1130168 and GNT1090116 Project Grants.