Practical considerations for epigenetic editing experiments and clinical applications

Abstract Background The discovery that CRISPR can be repurposed for targeted regulation of gene expression without inducing double-stranded breaks has paved the way for CRISPR-based epigenetic editing. Compared to other editing methods such as ZFPs and TALEs, CRISPR has the advantage of low cost, simplicity and multiplexing ability. Great strides have been made towards the clinical translation of these tools, and many recent studies have demonstrated long-lasting epigenetic changes in vivo, increasing the potential for therapeutically relevant outcomes. Main body On Addgene, there are currently > 700 different CRISPR-dCas9 tools available for CRISPR activation (CRISPRa), CRISPR interference (CRISPRi) and CRISPR-dCas9 epigenetics. Whilst this provides a broad range of tools to choose from, there is little consensus on which to use, when to use them, the cell types they are most suitable for, and how different epigenetic effectors interact with one another. Moreover, it is unclear how the existing epigenomic and transcriptomic contexts affect durability, efficiency and specificity of editing, raising further uncertainties about experimental design. Several unresolved questions remain: how many guides and effectors are required, what level of epigenetic change is required to exert functional outputs, and how does editing interact with other aspects of epigenetic and transcriptional machinery? Conclusions Our understanding of how epigenetic crosstalk contributes to epigenetic editing efficiency and how this informs experimental design is lagging. This review aims to highlight successes and challenges within the epigenetic editing field both in vitro and in vivo, providing a molecular framework of considerations for designing an editing experiment, focusing on the use of dCas9-based tools.