Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome

Elife. 2020 Mar 11;9:e52981. doi: 10.7554/eLife.52981.


Methylated cytosine is an effector of epigenetic gene regulation. In the brain, Dnmt3a is the sole 'writer' of atypical non-CpG methylation (mCH), and MeCP2 is the only known 'reader' for mCH. We asked if MeCP2 is the sole reader for Dnmt3a dependent methylation by comparing mice lacking either protein in GABAergic inhibitory neurons. Loss of either protein causes overlapping and distinct features from the behavioral to molecular level. Loss of Dnmt3a causes global loss of mCH and a subset of mCG sites resulting in more widespread transcriptional alterations and severe neurological dysfunction than MeCP2 loss. These data suggest that MeCP2 is responsible for reading only part of the Dnmt3a dependent methylation in the brain. Importantly, the impact of MeCP2 on genes differentially expressed in both models shows a strong dependence on mCH, but not Dnmt3a dependent mCG, consistent with mCH playing a central role in the pathogenesis of Rett Syndrome.

Keywords: Dnmt3a; MeCP2; Rett syndrome; chromosomes; gene expression; inhibitory neuron; mouse; neuroscience; non-CpG methylation.

Publication types

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

MeSH terms

  • Animals
  • DNA (Cytosine-5-)-Methyltransferases / genetics
  • DNA (Cytosine-5-)-Methyltransferases / metabolism*
  • DNA Methyltransferase 3A
  • Female
  • GABAergic Neurons / physiology*
  • Gene Expression Regulation, Developmental / physiology*
  • Genetic Predisposition to Disease
  • Male
  • Methyl-CpG-Binding Protein 2 / genetics
  • Methyl-CpG-Binding Protein 2 / metabolism*
  • Mice
  • Rett Syndrome / genetics
  • Rett Syndrome / metabolism*


  • DNMT3A protein, human
  • Dnmt3a protein, mouse
  • Mecp2 protein, mouse
  • Methyl-CpG-Binding Protein 2
  • DNA (Cytosine-5-)-Methyltransferases
  • DNA Methyltransferase 3A

Associated data

  • GEO/GSE124009
  • GEO/GSE123941
  • GEO/GSE103214