Harnessing DSB repair to promote efficient homology-dependent and -independent prime editing

• Published in: Nature communications Vol. 13; no. 1; p. 1240
• Main Authors: Peterka, Martin, Akrap, Nina, Li, Songyuan, Wimberger, Sandra, Hsieh, Pei-Pei, Degtev, Dmitrii, Bestas, Burcu, Barr, Jack, van de Plassche, Stijn, Mendoza-Garcia, Patricia, Šviković, Saša, Sienski, Grzegorz, Firth, Mike, Maresca, Marcello
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 24.03.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 45/23; 45/41; 631/337/1427/2191; 631/337/4041/3196; Animals; Biochemistry and Molecular Biology; Biokemi och molekylärbiologi; cleavage; CRISPR-Cas Systems; Deoxyribonucleic acid; DNA; DNA Breaks, Double-Stranded; DNA damage; DNA End-Joining Repair; DNA Repair; Double-strand break repair; Editing; Endonucleases - metabolism; Gene Editing; Genome editing; Genomes; Genomics; Homology; Humanities and Social Sciences; Mammalian cells; Mammals - genetics; multidisciplinary; Non-homologous end joining; Nuclease; pathway; Repair; RNA editing; Science; Science & Technology - Other Topics; Science (multidisciplinary); Yeast
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-28771-1

Prime editing recently emerged as a next-generation approach for precise genome editing. Here we exploit DNA double-strand break (DSB) repair to develop two strategies that install precise genomic insertions using an Sp Cas9 nuclease-based prime editor (PEn). We first demonstrate that PEn coupled to a regular prime editing guide RNA (pegRNA) efficiently promotes short genomic insertions through a homology-dependent DSB repair mechanism. While PEn editing leads to increased levels of by-products, it can rescue pegRNAs that perform poorly with a nickase-based prime editor. We also present a small molecule approach that yields increased product purity of PEn editing. Next, we develop a homology-independent PEn editing strategy, which installs genomic insertions at DSBs through the non-homologous end joining pathway (NHEJ). Lastly, we show that PEn-mediated insertions at DSBs prevent Cas9-induced large chromosomal deletions and provide evidence that continuous Cas9-mediated cutting is one of the mechanisms by which Cas9-induced large deletions arise. Altogether, this work expands the current prime editing toolbox by leveraging distinct DNA repair mechanisms including NHEJ, which represents the primary pathway of DSB repair in mammalian cells. Prime editing is a next-generation approach for precision genome engineering. Here the authors design a nuclease-based prime editor that leverages DNA repair pathways for targeted genomic insertions.