Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis

Life Science Alliance
Florian NoackFederico Calegari

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 neu...Continue Reading

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Citations

Apr 4, 2021·Cancers·Nguyen Thi Thanh HoKlaus Heese
Nov 23, 2021·Frontiers in Neuroscience·Julia Reichard, Geraldine Zimmer-Bensch

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Datasets Mentioned

BETA
GSE104585

Methods Mentioned

BETA
immunoprecipitation
amplicon sequencing
ChIP-seq
Fluorescence
PCR
BSamp-seq

Software Mentioned

HOMER
Diffbind
RepeatMasker
regioneR
MIRA
NGSplot
deepTools
MeDIP
UniPROBE
DAVID

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