De novo DNA methylation controls neuronal maturation during adult hippocampal neurogenesis [scRNA-seq]

Dynamic DNA methylation controls gene-regulatory networks underlying cell fate specification. How DNA methylation patterns change during adult hippocampal neurogenesis and their relevance for the generation of new neurons from adult neural stem cells has, however, remained unknown. Here, we show that neurogenesis-associated de novo DNA methylation is critical for maturation and functional integration of adult-born hippocampal neurons. Cell stage-specific bisulfite sequencing revealed a pronounced gain of DNA methylation at neuronal enhancers, gene bodies and binding sites of pro-neuronal transcription factors during adult neurogenesis, which mostly correlated with transcriptional up-regulation of the associated loci. Inducible deletion of both de novo DNA methyltransferases Dnmt3a and Dnmt3b in adult neural stem cells specifically impaired dendritic outgrowth and synaptogenesis of new neurons, resulting in impaired hippocampal excitability and specific deficits in hippocampus-dependent learning and memory. Our results highlight that, during adult neurogenesis, remodeling of neuronal methylomes is fundamental for proper hippocampal function. Hippocampal neural precursor cells were traced by injecting lentiviruses carrying a Cre-dependent Gfp vector into the dentate gyrus of nestin::Cre-ERT2(+/-)/Dnmt3a(fl/fl)-Dnmt3b(fl/fl) (KO) and nestin::Cre-ERT2(+/-)/Dnmt3a(wt/wt)-Dnmt3b(wt/wt) (WT) mice. Expression of Gfp and deletion of Dnmt3a/Dnmt3b were induced by administration of tamoxifen. Gfp-positive cells were isolated from the dentate gyrus of WT and KO mice by FACS after a chase period of four weeks (n = 4 mice per group).