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Genome-wide tracking of dCas9-methyltransferase footprints

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Galonska,  Christina
Dept. of Genome Regulation (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Charlton,  Jocelyn
Dept. of Genome Regulation (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society;
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA;

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Mattei,  Alexandra L.
Dept. of Genome Regulation (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society;
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA;
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA;

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Klages,  Sven
Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Timmermann,  Bernd
Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Meissner,  Alexander
Dept. of Genome Regulation (Head: Alexander Meissner), Max Planck Institute for Molecular Genetics, Max Planck Society;
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA;
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA;

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Citation

Galonska, C., Charlton, J., Mattei, A. L., Donaghey, J., Clement, K., Gu, H., et al. (2018). Genome-wide tracking of dCas9-methyltransferase footprints. Nature Communications, 9: 9:597. doi:10.1038/s41467-017-02708-5.


Cite as: https://hdl.handle.net/21.11116/0000-0000-7667-8
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.