Pioneer Factor Improves CRISPR-Based C-To-G and C-To-T Base Editing

Base editing events in eukaryote require a compatible chromatin environment, but there is little research on how chromatin factors contribute to the editing efficiency or window. By engineering BEs (base editors) fused with various pioneer factors, the authors found that SOX2 substantially increased the editing efficiency for GBE and CBE. While SoxN-GBE (SOX2-NH3-GBE) improved the editing efficiency at overall cytosines of the protospacer, SoxM-GBE/CBE (SOX2-Middle-GBE/CBE) enabled the higher base editing at PAM-proximal cytosines. By separating functional domains of SOX2, the SadN-GBE (SOX2 activation domain-NH3-GBE) is constructed for higher editing efficiency and SadM-CBE for broader editing window to date. With the DNase I assay, it is also proved the increased editing efficiency is most likely associated with the induction of chromatin accessibility by SAD. Finally, SadM-CBE is employed to introduce a stop codon in the proto-oncogene MYC, at a locus rarely edited by previous editors with high efficiency. In this work, a new class of pioneer-BEs is constructed by fusion of pioneer factor or its functional domains, which exhibits higher editing efficiency or broader editing window in eukaryote.

Automated summary

Base editing events in eukaryotes require a compatible chromatin environment, and this study investigates the contribution of chromatin factors to editing efficiency. The authors engineer base editors fused with various pioneer factors and find that SOX2 substantially increases editing efficiency. The study also demonstrates that the increased efficiency is likely associated with the induction of chromatin accessibility.