Tracking of dCas9-methyltransferase footprints

In normal mammalian development cytosine methylation is essential, and is directed to specific regions of the genome. Despite notable advances in mapping the genome-wide distribution, studying the direct contribution of DNA methylation to gene regulation has been limited by the lack of tools for its precise manipulation. Thus, combining the targeting capability of CRISPR/Cas9 systems 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-methyltransferase is challenging within a highly modified genome. To overcome this, we utilized an engineered, methylation depleted but maintenance competent mouse ES cell line and find a surprisingly ubiquitous nuclear activity of dCas9-methyltransferases. Our results provide new insights into the targeted regulation of DNA methylation and point to an important difference between genetic and epigenetic editing tools that require unique experimental considerations. Overall design: Here, we took advantage of an engineered cell line with little background DNA methylation (DKOzero) and performed transient transfections with dCas9-cat3a constructs in the presence of an sgRNA. We also created three doxycycline inducible constructs that when co-introduced with the reverse trans-activator (M2rtTA) enabled controlled expression of dCas9-cat3a (dCas9 fused to the catalytic domain of Dnmt3a), cat3a (the catalytic domain alone) or Dnmt3a (the full-length enzyme, including its N-terminal regulatory domain). We tested the dCas9-cat3a construct in the absence and presence of one or many sgRNAs. Finally, we perform transient transfection experiments of dCas9-cat3a with a guide RNA in the MCF7 and 293T cancer cell lines.