Abstract
Dynamic changes in DNA (hydroxy-)methylation are fundamental for stem cell differentiation. However, the signature of these epigenetic marks in specific cell types during corticogenesis is unknown. Moreover, site-specific manipulation of cytosine modifications is needed to reveal the significance and function of these changes. Here, we report the first assessment of (hydroxy-)methylation in neural stem cells, neurogenic progenitors, and newborn neurons during mammalian corticogenesis. We found that gain in hydroxymethylation and loss in methylation occur sequentially at specific cellular transitions during neurogenic commitment. We also found that these changes predominantly occur within enhancers of neurogenic genes up-regulated during neurogenesis and target of pioneer transcription factors. We further optimized the use of dCas9-Tet1 manipulation of (hydroxy-)methylation, locus-specifically, in vivo, showing the biological relevance of our observations for Dchs1, a regulator of corticogenesis involved in developmental malformations and cognitive impairment. Together, our data reveal the dynamics of cytosine modifications in lineage-related cell types, whereby methylation is reduced and hydroxymethylation gained during the neurogenic lineage concurrently with up-regulation of pioneer transcription factors and activation of enhancers for neurogenic genes.
Highlights
During embryonic development of the mammalian brain, neural stem and progenitor cells progressively switch from proliferative to differentiative divisions to generate neurons and glia that populate the cortical layers
We achieved both providing the first cell type–specific resource of 5(h)mC patterns in proliferative progenitors (PPs), differentiative progenitors (DPs), and neurons. This revealed that a commitment to neurogenesis in DP is characterized by an increase in 5hmC within enhancers of neurogenic genes and resulting in the subsequent loss in 5mC in their neuronal progeny. We found that these changes correlated with the (i) acquisition of histone marks characteristic of open chromatin, (ii) up-regulation and putative binding of basic helix-loop-helix pioneer transcription factors, and (iii) activation of their nearby neurogenic genes
Regulation of DNAmethylation in stem cells and its role in controlling gene expression during fate commitment have been the focus of many studies resulting in conflicting hypotheses with regard to the causes underlying these changes (Calo & Wysocka, 2013; Smith & Meissner, 2013; Schubeler, 2015; Atlasi & Stunnenberg, 2017)
Summary
During embryonic development of the mammalian brain, neural stem and progenitor cells progressively switch from proliferative to differentiative divisions to generate neurons and glia that populate the cortical layers. The majority (~80%) of basal progenitors are soon consumed to generate neurons, a subpopulation remains that undergoes a few rounds of symmetric proliferative divisions to expand their pool within the SVZ (Lui et al, 2011; Taverna et al, 2014) As a result, both proliferative progenitors (PPs) and differentiative progenitors (DPs) coexist as intermingled populations in the two germinal zones of the mammalian VZ and SVZ, whereas neurons are added to the cortical layers
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