CtIP promotes microhomology-mediated alternative end-joining during class switch recombination

Immunoglobulin heavy chain (Igh) class switch recombination (CSR) requires targeted introduction of DNA double strand breaks (DSBs) into repetitive “switch” region DNA elements in the Igh locus and subsequent ligation between distal DSBs. Both canonical non-homologous end-joining (C-NHEJ) that seals DNA ends with little or no homology, and a poorly defined alternative-end joining (A-NHEJ) process that requires microhomology ends for ligation have been implicated in CSR. Here we show that the DNA end-processing factor CtIP is required for microhomology-directed A-NHEJ during CSR. Additionally, we demonstrate that microhomology joins that are enriched upon depletion of C-NHEJ component Ku70 require CtIP. Finally, we show that CtIP binds to switch region DNA in an AID-dependent fashion. Our results establish CtIP as a bona fide component of microhomology-dependent A-NHEJ and unmask a hitherto unrecognized physiological role of microhomology-mediated end-joining in a C-NHEJ proficient environment.