CHARM and EvoETR: Precision epigenetic tools for gene silencing

With the advent of gene editing technologies like CRISPR/Cas9, it has become possible to edit genomic regions of interest for research and therapeutic purposes. These technologies have also been adapted to alter gene expression without changing their DNA sequence, allowing epigenetic edits. While genetic editors make edits by cutting the genome at specified regions, epigenetic editors leverage the same targeting mechanism but act based on the epigenetic modifier fused to them, such as a methyltransferase. Here, we discuss two recently employed epigenetic editors (epi‐editors) that silenced target genes involved in disease to mitigate their effects. Neumann et al. reported the construction of an epigenetic editor called CHARM that could methylate and silence the prion gene in mouse brains and subsequently switch itself off. Additionally, Capelluti et al. developed an epi‐editor called EvoETR that knocked down Pcsk9 in the murine liver to reduce LDL levels. We aim to highlight the design principles underlying the design of these epi‐editors to inform future editor designs. (A) CRISPR/Cas9 cuts DNA at specific sites, performing traditional gene editing. dCas9, a catalytically inactive version, binds to DNA without cutting and alters gene expression. (B) The Prnp gene in the brain was silenced by CHARM, which recruits DNMT3A to methylate the gene, delivered via CRISPR/dCas9 or ZFPs/TALEs, effectively reducing prion protein expression. (C) EvoETR targets the Pcsk9 gene in the liver using ZFPs fused to DNMT3A and DNMT3L to methylate and silence the gene, lowering LDL cholesterol levels without DNA breaks. (D) TALEs, ZFPs, and dCas9 are shown as interchangeable tools for epigenetic editing, capable of being fused with repressive domains to silence genes, offering flexible gene silencing strategies.