Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors

• Published in: Nature communications Vol. 15; no. 1; pp. 5611 - 13
• Main Authors: Hu, Qing, Espejo Valle-Inclán, Jose, Dahiya, Rashmi, Guyer, Alison, Mazzagatti, Alice, Maurais, Elizabeth G., Engel, Justin L., Lu, Huiming, Davis, Anthony J., Cortés-Ciriano, Isidro, Ly, Peter
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 04-07-2024; Nature Publishing Group; Nature Portfolio
• Subjects: 13; 13/106; 14; 14/32; 14/63; 45/23; 631/208/1405; 631/208/211; 631/67/68; 631/80/103; 631/80/641/2002; Cell cycle; Chromosome deletion; Chromosomes; Chromothripsis; CRISPR; CRISPR-Cas Systems; DNA Breaks, Double-Stranded; DNA damage; DNA End-Joining Repair; DNA fragmentation; DNA repair; Double-strand break repair; Errors; Fragmentation; Gene Rearrangement; Genomics; Humanities and Social Sciences; Humans; Kinetics; Micronuclei; Micronuclei, Chromosome-Defective; Mitosis - genetics; multidisciplinary; Non-homologous end joining; Science; Science (multidisciplinary); Tumor Suppressor p53-Binding Protein 1 - genetics; Tumor Suppressor p53-Binding Protein 1 - metabolism; Yeast
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-49985-5

Mitotic errors generate micronuclei entrapping mis-segregated chromosomes, which are susceptible to catastrophic fragmentation through chromothripsis. The reassembly of fragmented chromosomes by error-prone DNA double-strand break (DSB) repair generates diverse genomic rearrangements associated with human diseases. How specific repair pathways recognize and process these lesions remains poorly understood. Here we use CRISPR/Cas9 to systematically inactivate distinct DSB repair pathways and interrogate the rearrangement landscape of fragmented chromosomes. Deletion of canonical non-homologous end joining (NHEJ) components substantially reduces complex rearrangements and shifts the rearrangement landscape toward simple alterations without the characteristic patterns of chromothripsis. Following reincorporation into the nucleus, fragmented chromosomes localize within sub-nuclear micronuclei bodies (MN bodies) and undergo ligation by NHEJ within a single cell cycle. In the absence of NHEJ, chromosome fragments are rarely engaged by alternative end-joining or recombination-based mechanisms, resulting in delayed repair kinetics, persistent 53BP1-labeled MN bodies, and cell cycle arrest. Thus, we provide evidence supporting NHEJ as the exclusive DSB repair pathway generating complex rearrangements from mitotic errors.
Mitotic errors promote chromosome fragmentation and rearrangements through chromothripsis. Here, the authors identify NHEJ as the primary DSB repair pathway underlying chromothripsis and investigate the kinetics of fragment reassembly across the cell cycle.