Epigenetic switch reveals CRISPR/Cas9 response to cytosine methylation in plants: Comment

Commentary on Přibylová et al. (2022). 235 p 2285-2299

Genome editing techniques, such as the CRISPR/Cas9 system, offer a game-changing opportunity for crop improvement by enabling precise modifications to be made at targeted genomic loci. The CRISPR/Cas9 system has been employed successfully in many plant species; however, in order to use the system to its full potential, it is important to understand precisely how it functions and the factors that may limit its effectiveness. The mechanistic details of Cas9-induced double-strand breaks (DSBs), which underpin the mutational ability of the system, have been well described. It is also known that the efficiency of editing varies for different target sequences. However, the impact of epigenetic modifications on CRISPR/Cas9 efficacy and subsequent DNA repair is poorly understood, especially in plants. Epigenetic modifications affect gene regulation and genome stability. As such, the epigenetic status of an editing target site may influence the frequency of CRISPR/Cas9-induced mutations, for example by affecting how well Cas9 binds and cuts, or the efficiency and accuracy of DNA repair mechanisms. Genome-wide analyses have shown the efficiency of CRISPR/Cas9 editing to be lower for heterochromatin than euchromatin (Daer et al., 2017), although this is still contested (Kallimasioti-Pazi et al., 2018). However, comparisons of editing efficiencies between heterochromatin and euchromatin have involved the analysis of two or more loci, and different target loci vary in more than just their epigenetic status. In this issue of New Phytologist, Přibylová et al. (2022) investigate the effect of cytosine methylation on the generation of CRISPR/Cas9-induced mutations at multiple target sites within the same locus in Nicotiana benthamiana, using a virus-based epigenetic switch. This epigenetic switch allows for the conversion of the chromatin state of the target locus and so can be used to shed light on how cytosine methylation affects the frequency and outcome of CRISPR/Cas9 induced editing at a single site. The authors also highlighted the important role of single-nucleotide microhomology-mediated DNA repair in genome editing.