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Nat Commun. 2018 Feb 9;9(1):597. doi: 10.1038/s41467-017-02708-5.

Genome-wide tracking of dCas9-methyltransferase footprints.

Author information

1
Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.
2
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
3
Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
4
Armenise-Harvard Laboratory of Integrative Genomics, Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, 80078, Italy.
5
Translational Hepatology and Stem Cell Biology, Hannover Medical School, Hannover, 30625, Germany.
6
Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, 48149, Germany.
7
Department for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, 80804, Germany.
8
Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany. meissner@molgen.mpg.de.
9
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. meissner@molgen.mpg.de.
10
Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. meissner@molgen.mpg.de.

Abstract

In normal mammalian development cytosine methylation is essential and is directed to specific regions of the genome. Despite notable advances through mapping its genome-wide distribution, studying the direct contribution of DNA methylation to gene and genome regulation has been limited by the lack of tools for its precise manipulation. Thus, combining the targeting capability of the CRISPR-Cas9 system with an epigenetic modifier has attracted interest in the scientific community. In contrast to profiling the genome-wide cleavage of a nuclease competent Cas9, tracing the global activity of a dead Cas9 (dCas9) methyltransferase fusion protein is challenging within a highly methylated genome. Here, we report the generation and use of an engineered, methylation depleted but maintenance competent mouse ES cell line and find surprisingly ubiquitous nuclear activity of dCas9-methyltransferases. Subsequent experiments in human somatic cells refine these observations and point to an important difference between genetic and epigenetic editing tools that require unique experimental considerations.

PMID:
29426832
PMCID:
PMC5807365
DOI:
10.1038/s41467-017-02708-5
[Indexed for MEDLINE]
Free PMC Article

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