Epigenetically bistable regions across neuron-specific genes govern neuron eligibility to a coding ensemble in the hippocampus

Sensory inputs activate sparse ensembles of neurons in the dentate gyrus of the hippocampus, but how eligibility of individual neurons to recruitment is determined remains elusive. We identified thousands of largely bistable (CpG methylated or unmethylated) regions within neuronal gene bodies, established during mouse dentate gyrus development. Reducing DNA methylation and the proportion of the methylated epialleles at bistable regions compromised novel context-induced neuronal activation. Conversely, increasing methylation and the frequency of the methylated epialleles at bistable regions enhanced intrinsic excitability. Single-nuclei profiling revealed enrichment of specific epialleles from a subset of bistable regions in activated neurons. Genes displaying both differential methylation and expression in activated neurons defined a network of proteins regulating neuronal excitability and structural plasticity. We propose a model in which bistable regions create neuron heterogeneity, and constellations of exonic epialleles dictate, via modulating gene expression and neuronal excitability, eligibility to a coding ensemble Compared tissue and cells from dorsal dentate gyrus C57BL6 male animals that were either injected with an AAV-DJ-SYN-DNMT3A virus, control animals, or animals exposed to a novel environment for 15 minutes. Bulk RRBS DNA methylation, single nuclei DNA methylation, and single nuclei RNA expression profiles were collected.