scNMT-seq of the adult NSC lineage - RNA

Stem cells in the adult brain are specialized astrocytes capable of generating neurons and glial cells. While neural stem cells (NSCs) and common astrocytes have clearly distinct functions, they share highly similar transcriptome profiles. How stemness is molecularly encoded is therefore unclear. Here we use single-cell NMT-seq to simultaneously characterize the transcriptome, DNA methylome and chromatin accessibility of astrocytes and the NSC lineage in the healthy and ischemic brain. Our data reveal distinct methylation profiles associated with either astrocyte or stem cell function. Stemness is conferred by methylation of astrocyte genes and demethylation of neurogenic genes that are expressed only later. Surprisingly, ischemic injury unlocks the stemness-methylome in common astrocytes enabling generation of neuroblasts. Furthermore, we show that oligodendrocytes employ Tet-mediated demethylation to regulate expression of myelin-related genes, many of which are abnormally methylated in multiple sclerosis. Overall, we show that DNA methylation is a promising target for regenerative medicine. Overall design: Astrocytes, oligodendrocytes, adult neural stem cells as well as their progeny were isolated via flourescence-activated cell sorting (FACS) from the ventricular-subventricular zone, striatum, and olfactory bulb. Each biological replicate (pA, pB, …) consists of one or more mice. Cells were subjected to scNMT-seq in order to quantify DNA methylation, chromatin accessibility, and gene expression at single cell resolution.