CtIP Maintains Stability at Common Fragile Sites and Inverted Repeats by End Resection-Independent Endonuclease Activity

Chromosomal rearrangements often occur at genomic loci with DNA secondary structures, such as common fragile sites (CFSs) and palindromic repeats. We developed assays in mammalian cells that revealed CFS-derived AT-rich sequences and inverted Alu repeats (Alu-IRs) are mitotic recombination hotspots, requiring the repair functions of carboxy-terminal binding protein (CtBP)-interacting protein (CtIP) and the Mre11/Rad50/Nbs1 complex (MRN). We also identified an endonuclease activity of CtIP that is dispensable for end resection and homologous recombination (HR) at I-SceI-generated “clean” double-strand breaks (DSBs) but is required for repair of DSBs occurring at CFS-derived AT-rich sequences. In addition, CtIP nuclease-defective mutants are impaired in Alu-IRs-induced mitotic recombination. These studies suggest that an end resection-independent CtIP function is important for processing DSB ends with secondary structures to promote HR. Furthermore, our studies uncover an important role of MRN, CtIP, and their associated nuclease activities in protecting CFSs in mammalian cells. [Display omitted] •AT-rich CFS sequences and inverted Alu repeats induce mitotic recombination•Human CtIP exhibits an endonuclease activity that is dispensable for end resection•The CtIP endonuclease activity is required for repairing structure-forming DSBs•The nuclease activities of CtIP and Mre11 are important for CFS protection Chromosomal rearrangements are tightly associated with cancer and often occur in regions containing DNA secondary structures, such as common fragile sites (CFSs) and palindromic repeats. Wang et al. show that CtIP and the MRN complex function to remove secondary DNA structures to repair chromosomal double-strand breaks and protect CFSs in mammals.