Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning

Programmable C center dot G-to-G center dot C base editors (CGBEs) have broad scientific and therapeutic potential, but their editing outcomes have proved difficult to predict and their editing efficiency and product purity are often low. We describe a suite of engineered CGBEs paired with machine learning models to enable efficient, high-purity C center dot G-to-G center dot C base editing. We performed a CRISPR interference (CRISPRi) screen targeting DNA repair genes to identify factors that affect C center dot G-to-G center dot C editing outcomes and used these insights to develop CGBEs with diverse editing profiles. We characterized ten promising CGBEs on a library of 10,638 genomically integrated target sites in mammalian cells and trained machine learning models that accurately predict the purity and yield of editing outcomes (R = 0.90) using these data. These CGBEs enable correction to the wild-type coding sequence of 546 disease-related transversion single-nucleotide variants (SNVs) with >90% precision (mean 96%) and up to 70% efficiency (mean 14%). Computational prediction of optimal CGBE-single-guide RNA pairs enables high-purity transversion base editing at over fourfold more target sites than achieved using any single CGBE variant. Efficiency of transversion base editing is increased by matching a set of base editors to target sequences.

Automated summary

Engineered CGBEs paired with machine learning models have been developed to enable efficient and high-purity base editing, correcting disease-related SNVs with precision and increasing editing efficiency. Matching a set of base editors to target sequences can further enhance transversion base editing efficiency.