The 3′-flap endonuclease XPF-ERCC1 promotes alternative end joining and chromosomal translocation during B cell class switching

Robust alternative end joining (A-EJ) in classical non-homologous end joining (c-NHEJ)-deficient murine cells features double-strand break (DSB) end resection and microhomology (MH) usage and promotes chromosomal translocation. The activities responsible for removing 3′ single-strand overhangs following resection and MH annealing in A-EJ remain unclear. We show that, during class switch recombination (CSR) in mature mouse B cells, the structure-specific endonuclease complex XPF-ERCC1SLX4, although not required for normal CSR, represents a nucleotide-excision-repair-independent 3′ flap removal activity for A-EJ-mediated CSR. B cells deficient in DNA ligase 4 and XPF-ERCC1 exhibit further impaired class switching, reducing joining to the resected S region DSBs without altering the MH pattern in S-S junctions. In ERCC1-deficient A-EJ cells, 3′ single-stranded DNA (ssDNA) flaps that are generated predominantly in S/G2 phase of the cell cycle are susceptible to nuclease resolution. Moreover, ERCC1 promotes c-myc-IgH translocation in Lig4−/− cells. Our study reveals an important role of the flap endonuclease XPF-ERCC1 in A-EJ and oncogenic translocation in mouse B cells. [Display omitted] •XPF-ERCC1 deficiency impairs alternative end joining (A-EJ)-mediated class switching•3′ flap endonuclease, but not NER function of XPF-ERCC1, is required for A-EJ•Loss of ERCC1 impedes joining of resected 3′ flap DSB ends•ERCC1 enhances c-myc-IgH translocation in Lig4-deficient cells Bai et al. show that the 3′ flap endonuclease XPF-ERCC1, together with SLX4, is required for alternative end joining (A-EJ)-mediated class switching in mouse B cells. XPF-ERCC1 removes 3′ single-strand overhangs formed after end resection and microhomology annealing. Moreover, ERCC1 promotes c-myc-IgH translocations in A-EJ.