,Improving Plant Genome Editing with High-Fidelity xCas9 and Non-canonical PAM-Targeting Cas9-NG

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Two recently engineered SpCas9 variants,namely xCas9 and Cas9-NG,show promising potential in improving targeting specificity and broadening the targeting range.In this study,we evaluated these Cas9 variants in the model and crop plant,rice.We first tested xCas9-3.7,the most effective xCas9 variant in mammalian cells,for targeted mutagenesis at 16 possible NGN PAM (protospacer adjacent motif) combinations in duplicates,xCas9 exhibited nearly equivalent editing efficiency to wild-type Cas9 (Cas9-WT) at most canonical NGG PAM sites tested,whereas it showed limited activity at non-canonical NGH (H =A,C,T) PAM sites.High editing efficiency of xCas9 at NGG PAMs was further demonstrated with C to T base editing by both rAPOBEC1 and PmCDA1 cytidine deaminases.With mismatched sgRNAs,we found that xCas9 had improved targeting specificity over the Cas9-WT.Furthermore,we tested two Cas9-NG variants,Cas9-NGv1 and Cas9-NG,for targeting NGN PAMs.Both Cas9-NG variants showed higher editing efficiency at most non-canonical NG PAM sites tested,and enabled much more efficient editing than xCas9 at AT-rich PAM sites such as GAT,GAA,and CAA.Nevertheless,we found that Cas9-NG variants showed significant reduced activity at the canonical NGG PAM sites.In stable transgenic rice lines,we demonstrated that Cas9-NG had much higher editing efficiency than Cas9-NGv1 and xCas9 at NG PAM sites.To expand the base-editing scope,we developed an efficient C to T base-editing system by making fusion of Cas9-NG nickase (D10A version),PmCDA1,and UGI.Taken together,our work benchmarked xCas9 as a high-fidelity nuclease for targeting canonical NGG PAMs and Cas9-NG as a preferred variant for targeting relaxed PAMs for plant genome editing.
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