Silencing of human HTT by targeted CRISPR/dCas9-mediated epigenetic editing

Background Gene silencing is widely recognized as a promising therapeutic approach for dominant monogenic disorders. Current silencing strategies, many of which are transient, utilize RNA interference. Gene silencing may also be achieved through directed epigenetic editing using a CRISPR/dCas9 effector fused to DNA methyltransferase 3A (dCas9-DNMT3A). We used this system to direct DNA methylation to HTT , the causal gene underlying the autosomal dominant neurodegenerative disorder Huntington's disease, to assess the translational potential of this strategy for treating a genetic neurological disease. Objective To characterize the regulatory effect of targeted dCas9-DNMT3A-mediated DNA methylation at HTT . Methods We exploited DNA methylation profiles of high and low HTT -expressing tissues and targeted hypomethylated regions of HTT associated with high levels of HTT expression. Results De novo DNA methylation of loci within defined upstream, promoter, intragenic and downstream regions of HTT resulted in robust, acute silencing of HTT . The best long-term silencing of HTT , which persisted up to 30 days, was observed when targeted DNA methylation was directed to the 5’UTR and promoter regions of HTT . Conclusions HTT gene silencing may be achieved via targeted de novo DNA methylation within hypomethylated regulatory regions at the HTT locus. DNA methylation editing may be an attractive therapeutic approach for Huntington disease due to its potential for long-term silencing and reversibility.