De novo DNA methylation controls neuronal maturation during adult hippocampal neurogenesis [Dnmt_inVitro_RRBS]

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. Overall design: Neural precursor cell (NPC) cultures were generated from micro-dissected dentate gyrus tissue of nestin::CreERT2(-/-)-Dnmt3a-2lox-Dnmt3b-2lox one week after tamoxifen administration. NPC cultures were genotyped at Dnmt3a and Dnmt3b alleles and wildtype (WT) and double knock-out cultures (KO) were expanded and differentiated for five days to generate neurons. DNA methylation profiling was performed by RRBS on WT and KO NPCs and FAC-sorted neurons.