Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

Methylation and the single neuronal cell The presence or absence of methylation on chromosomal DNA can drive or repress gene expression. Now, a comprehensive map of methylation variation in neuronal cell populations, including a between-species comparison, illustrates how epigenetic diversity plays important roles in neuronal development. Luo et al. examined how DNA methylation is both similar and different within neurons at the single-nucleus level in humans and mice. They identified 16 mouse and 21 human neuronal clusters, with greater complexity of excitatory neurons in deep brain layers than in superficial layers. Science, this issue p. 600 Single-nucleus methylomes distinguish neuron types and predict conserved gene regulatory elements in mice and humans. The mammalian brain contains diverse neuronal types, yet we lack single-cell epigenomic assays that are able to identify and characterize them. DNA methylation is a stable epigenetic mark that distinguishes cell types and marks regulatory elements. We generated >6000 methylomes from single neuronal nuclei and used them to identify 16 mouse and 21 human neuronal subpopulations in the frontal cortex. CG and non-CG methylation exhibited cell type–specific distributions, and we identified regulatory elements with differential methylation across neuron types. Methylation signatures identified a layer 6 excitatory neuron subtype and a unique human parvalbumin-expressing inhibitory neuron subtype. We observed stronger cross-species conservation of regulatory elements in inhibitory neurons than in excitatory neurons. Single-nucleus methylomes expand the atlas of brain cell types and identify regulatory elements that drive conserved brain cell diversity.

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