SauCas9-based cell cycle-dependent genome editing via AAV delivery

The CRISPR-Cas system is a widely used genome editing technology with diverse applications. Although homology-directed repair (HDR) offers precise gene editing, its efficiency is typically lower than that of non-homologous end joining (NHEJ). Building on our previous cell cycle-dependent genome editing system for Streptococcus pyogenes Cas9 (SpyCas9), we adopted this approach for Staphylococcus aureus Cas9 (SauCas9) to enable efficient adeno-associated virus (AAV) delivery. To enhance HDR efficiency and editing accuracy in the context of AAV delivery, we developed a cell cycle-dependent genome editing system. We screened 10 anti-CRISPR (Acr) candidates and identified AcrIIA5, A13, A14, A15, and C1 as potent inhibitors of SauCas9. The fusion of these Acrs with the Cdt1(30-120) fragment restricted SauCas9 activity to the S/G2 phases, where HDR is predominant. Although AcrIIA11 and AcrIIA16 alone showed weak inhibition, their Cdt1 fusions (AcrIIA11+Cdt1 and AcrIIA16+Cdt1) showed a 2-fold increase in HDR efficiency within the AAV delivery system. This AAV-based, cell cycle-dependent SauCas9 system, which leverages optimized Acr-Cdt1 fusions, holds promise for improving the efficiency and accuracy of in vivo genome editing. Its small size is ideal for AAV packaging and may offer fewer off-target effects.