Single C-to-T substitution using engineered APOBEC3G-nCas9 base editors with minimum genome- and transcriptome-wide off-targets

Bystander editing occurs when cytosine base editors edit nearby Cs other than the target C within their activity windows. To address a challenging case in which a bystander C lies immediately upstream of the target C, we identified and engineered the APOBEC3G (A3G) cytosine deaminase to develop base editor variants A3G-BEs that preferentially edit the second C in the 5'-CC-3' motif. We discovered our A3G-BE variants exhibit high efficiency and sequence-specificity in many endogenous sites of human cells, and maintain the baseline activities of widespread off-target editing in cellular DNA and RNA.