Improvement of precise large-fragment deletion with a versatile nuclease prime editor

Among 241,074 known pathogenic or likely pathogenic human genetic variants, ~27.7% were deletions or replacements (i.e., insertions following deletions) 1 . Many abnormal deletions and replacements involved relatively large DNA fragments, including ~953 variants with deletions exceeding 1 kb (Supplementary Fig. S1a ), posing a major challenge for genome editing. The prime editing (PE) system represented a significant breakthrough for diverse genome editing, while it was limited for deleting larger DNA fragments 2 , 3 . The recently reported nuclease-based prime editor (PEn) combined with paired pegRNAs provided a novel prime editing tool for large-fragment deletions and simultaneous insertions 4 , 5 . However, the current platforms based on PEn still exhibited overall suboptimal efficiencies and produced unwanted edits, significantly hindering the applicability of this versatile tool.