GSE137098
Embryonic stem cell-derived neurons as a model system for epigenome maturation during development
DNA methylation in neurons is directly linked to neuronal genome regulation and maturation. Unlike other tissues, vertebrate neurons accumulate high levels of atypical DNA methylation in the CH sequence context (mCH) during early postnatal brain development. Here we investigate to what extent neurons derived in vitro from both mouse and human pluripotent stem cells recapitulate in vivo DNA methylation patterns. While human ESC-derived neurons did not accumulate mCH in either 2D culture or 3D organoid models, even after prolonged culture, neurons derived from mouse ESCs in vitro acquire in vivo levels of mCH over a similar time period as both primary neuron cultures and in vivo development. mESC-derived neuron mCH deposition occurs concurrently with a transient increase in Dnmt3a expression, is preceded by expression of the post-mitotic marker Rbfox3 (NeuN), is enriched at the nuclear lamina, and negatively correlates with gene expression. We further show that CG- and CH-methylation patterning subtly differs between in vitro mES-derived and in vivo neurons, suggesting the involvement of additional non-cell autonomous processes. As our findings show mouse ESC-derived neurons are capable of recapitulating the unique DNA methylation landscape of adult mammalian neurons in vitro over experimentally tractable timeframes, identification of such external cues, and elucidation of the writing-reading mechanisms and functional consequences of these different types and patterns of DNA methylation events, is now achievable. Overall design: Whole genome bisulfite sequencing of 49 different mouse cell culture and primary cell samples, and RNA-seq of a subset of samples