Ezh2 dCas9 and KRAB dCas9 enable engineering of epigenetic memory in a context dependent manner
BackgroundRewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve in a predictable manner using targeted systems.ResultsHere, we report that persistent epigenetic memory required both a DNA methyltransferase (DNMT3A dCas9) and a histone methyltransferase (Ezh2 dCas9 or KRAB dCas9) We demonstrate that the histone methyltransferase requirement can be locus specific. Co targeting Ezh2 dCas9, but not KRAB dCas9, with DNMT3A dCas9 and DNMT3L induced long term HER2 repression over at least 50 days (approximately 57 cell divisions) and triggered an epigenetic switch to a heterochromatic environment. An increase in H3K27 trimethylation and DNA methylation was stably maintained and accompanied by a sustained loss of H3K27 acetylation. Interestingly, substitution of Ezh2 dCas9 with KRAB dCas9 enabled long term repression at some target genes (e.g. SNURF) but not at HER2, at which H3K9me3 and DNA methylation were transiently acquired and subsequently lost. Off target DNA hypermethylation occurred at many individual CpG sites but rarely at multiple CpGs in a single promoter, consistent with no detectable effect on transcription at the off target loci tested. Conversely, robust hypermethylation was observed at HER2. We further demonstrated that Ezh2 dCas9 required full length DNMT3L for maximal activity and that co targeting DNMT3L was sufficient for persistent repression by Ezh2 dCas9 or KRAB dCas9.ConclusionsThese data demonstrate that targeting different combinations of histone and DNA methyltransferases is required to achieve maximal repression at different loci. Fine tuning of targeting tools is a necessity to engineer epigenetic memory at any given locus in any given cell type.
Epigenetics Chromatin