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Cell Stem Cell. 2018 Apr 5;22(4):559-574.e9. doi: 10.1016/j.stem.2018.02.012. Epub 2018 Mar 15.

Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology.

Author information

1
Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany.
2
The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
3
Department of Biomedical and Pharmaceutical Sciences, George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI 02881, USA.
4
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
5
Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany.
6
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
7
Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
8
Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
9
Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
10
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: meissner@molgen.mpg.de.
11
The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA. Electronic address: evangelos.kiskinis@northwestern.edu.

Abstract

The somatic DNA methylation (DNAme) landscape is established early in development but remains highly dynamic within focal regions that overlap with gene regulatory elements. The significance of these dynamic changes, particularly in the central nervous system, remains unresolved. Here, we utilize a powerful human embryonic stem cell differentiation model for the generation of motor neurons (MNs) in combination with genetic mutations in the de novo DNAme machinery. We quantitatively dissect the role of DNAme in directing somatic cell fate with high-resolution genome-wide bisulfite-, bulk-, and single-cell-RNA sequencing. We find defects in neuralization and MN differentiation in DNMT3A knockouts (KO) that can be rescued by the targeting of DNAme to key developmental loci using catalytically inactive dCas9. We also find decreased dendritic arborization and altered electrophysiological properties in DNMT3A KO MNs. Our work provides a list of DNMT3A-regulated targets and a mechanistic link between de novo DNAme, cellular differentiation, and human MN function.

KEYWORDS:

DNA methylation; DNMT3A; ESCs; cell fate; epigenetics; motor neurons; neurogenesis; spinal cord development

PMID:
29551301
PMCID:
PMC6535433
DOI:
10.1016/j.stem.2018.02.012
[Indexed for MEDLINE]
Free PMC Article

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