Principle of DNA Double Strand Breaks clustering revealed by Capture-HiC

Translocations, that occur when two DNA Double Strand breaks (DSBs) are abnormally rejoined, represent highly deleterious genome rearrangements favoring cancer apparition and progression. However, the mechanisms that drive their formation are yet poorly deciphered. One prerequisite for translocation is the juxtaposition of two spatially distant DSBs, an event that may arise if DSBs coalesce within a repair center. Although largely accepted in yeast, DSB clustering is still subjected to intense debate in higher eukaryotes. Using a cell line where multiple DSBs are induced at specific and annotated genomic positions throughout the human genome, combined with High Throughput Chromosome Conformation Capture (Hi-C) followed by sequence capture and deep sequencing (Capture Hi-C) we report here fundamental principles of DSB clustering in human cells. We found that DSBs exhibit clustering only if induced in transcriptionally active genes. Clustering of damaged genes mainly occur during the G1 cell cycle phase and coincide with a lack of repair. Moreover DSB clustering depends on the MRN complex, as well as the Formin 2 (FMN2) nuclear actin organizer and the LINC (LInker of Nuclear and Cytoplasmic skeleton) complex, suggesting that active mechanisms promote DSB clustering. This work reveals that when damaged, active genes exhibit a very peculiar behavior compared to the rest of the genome, being mostly left unrepaired and clustered in G1 while being repaired by homologous recombination in post-replicative cells.