HLTF disrupts Cas9-DNA post-cleavage complexes to allow DNA break processing

• Published in: Nature communications 2024-07, Vol.15 (1), p.5789-18, Article 5789
• Main Authors: Reginato, Giordano, Dello Stritto, Maria Rosaria, Wang, Yanbo, Hao, Jingzhou, Pavani, Raphael, Schmitz, Michael, Halder, Swagata, Morin, Vincent, Cannavo, Elda, Ceppi, Ilaria, Braunshier, Stefan, Acharya, Ananya, Ropars, Virginie, Charbonnier, Jean-Baptiste, Jinek, Martin, Nussenzweig, Andrè, Ha, Taekjip, Cejka, Petr
• Format: Article
• Language: English
• Subjects: 631/208/4041/3196; 631/45/147; 631/45/173; 631/57/2265; 82/29; 82/83; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Chemical reactions; Cleavage; CRISPR; CRISPR-Associated Protein 9 - genetics; CRISPR-Associated Protein 9 - metabolism; CRISPR-Associated Proteins - genetics; CRISPR-Associated Proteins - metabolism; CRISPR-Cas Systems; Deoxyribonucleic acid; DNA; DNA - genetics; DNA - metabolism; DNA Breaks, Double-Stranded; DNA Cleavage; DNA damage; DNA End-Joining Repair; DNA repair; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Double-strand break repair; Endodeoxyribonucleases - genetics; Endodeoxyribonucleases - metabolism; Endonuclease; Endonucleases - genetics; Endonucleases - metabolism; Gene Editing; Genetic modification; Genome editing; Homology; Humanities and Social Sciences; Humans; MRE11 Homologue Protein - genetics; MRE11 Homologue Protein - metabolism; MRE11 protein; multidisciplinary; Non-homologous end joining; Science; Science (multidisciplinary); Transcription Factors - genetics; Transcription Factors - metabolism; Translocase; Yeast
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-50080-y

The outcome of CRISPR-Cas-mediated genome modifications is dependent on DNA double-strand break (DSB) processing and repair pathway choice. Homology-directed repair (HDR) of protein-blocked DSBs requires DNA end resection that is initiated by the endonuclease activity of the MRE11 complex. Using reconstituted reactions, we show that Cas9 breaks are unexpectedly not directly resectable by the MRE11 complex. In contrast, breaks catalyzed by Cas12a are readily processed. Cas9, unlike Cas12a, bridges the broken ends, preventing DSB detection and processing by MRE11. We demonstrate that Cas9 must be dislocated after DNA cleavage to allow DNA end resection and repair. Using single molecule and bulk biochemical assays, we next find that the HLTF translocase directly removes Cas9 from broken ends, which allows DSB processing by DNA end resection or non-homologous end-joining machineries. Mechanistically, the activity of HLTF requires its HIRAN domain and the release of the 3′-end generated by the cleavage of the non-target DNA strand by the Cas9 RuvC domain. Consequently, HLTF removes the H840A but not the D10A Cas9 nickase. The removal of Cas9 H840A by HLTF explains the different cellular impact of the two Cas9 nickase variants in human cells, with potential implications for gene editing. Cas9 remains bound to DNA after cleavage and its removal is required for DNA double-strand break repair. Here, the authors show that the HLTF translocase disrupts the Cas9- DNA post-cleavage complexes in a process that requires the HLTF HIRAN domain and ATPase activity.