Aberrant recombination and repair during immunoglobulin class switching in BRCA1-deficient human B cells

Breast cancer type 1 susceptibility protein (BRCA1) has a multitude of functions that contribute to genome integrity and tumor suppression. Its participation in the repair of DNA double-strand breaks (DSBs) during homologous recombination (HR) is well recognized, whereas its involvement in the second major DSB repair pathway, nonhomologous end-joining (NHEJ), remains controversial. Here we have studied the role of BRCA1 in the repair of DSBs in switch (S) regions during immunoglobulin class switch recombination, a physiological, deletion/recombination process that relies on the classical NHEJ machinery. A shift to the use of microhomology-based, alternative end-joining (A-EJ) and increased frequencies of intra-S region deletions as well as insertions of inverted S sequences were observed at the recombination junctions amplified from BRCA1-deficient human B cells. Furthermore, increased use of long microhomologies was found at recombination junctions derived from E3 ubiquitin-protein ligase RNF168-deficient, Fanconi anemia group J protein (FACJ, BRIP1)-deficient, or DNA endonuclease RBBP8 (CtIP)-compromised cells, whereas an increased frequency of S-region inversions was observed in breast cancer type 2 susceptibility protein (BRCA2)-deficient cells. Thus, BRCA1, together with its interaction partners, seems to play an important role in repairing DSBs generated during class switch recombination by promoting the classical NHEJ pathway. This may not only provide a general mechanism underlying BRCA1’s function in maintaining genome stability and tumor suppression but may also point to a previously unrecognized role of BRCA1 in B-cell lymphomagenesis. Significance DNA double-strand breaks (DSBs) are one of the most deleterious types of DNA lesions and may pose a severe threat to genome integrity. Breast cancer type 1 susceptibility protein (BRCA1) is a multifunctional DNA damage response factor that is known to protect the chromosome/genome stability by participating in one of the major DSB repair pathways, homologous recombination (HR). Here we show that in human B cells BRCA1 is also required for another major DSB repair pathway, nonhomologous end-joining (NHEJ) during immunoglobulin class switch recombination (CSR), probably by inhibition of resection and microhomology-mediated end-joining (MMEJ), as well as promotion of long-range recombination. Our study provides previously unrecognized insights into BRCA1’s function in maintaining genome stability and tum