BRIP1, a G-quadruplex DNA helicase, protects against AID-induced genomic instability by limiting R-loop accumulation

BRIP1 (BRCA1-interacting protein 1) or FANCJ is a 5′–3′ DNA helicase that plays critical roles in the maintenance of genome stability through its involvement in DNA repair, replication stress responses, and the resolution of DNA secondary structures or non-B DNAs. Defects in the BRIP1 helicase gene are associated with an increased risk of various cancers. It has been shown that BRIP1-deficient mice are predisposed to B-cell lymphoma. Because activation-induced cytidine deaminase (AID)-dependent genomic instability resulting from its mistargeting to non-immunoglobulin genes is a major hallmark of B-cell lymphoma, and non-B DNA structures, including G-quadruplexes (G4) and RNA–DNA hybrids (R-loops), are implicated in AID-induced genomic instability, we asked whether BRIP1 helicase limits these secondary structures to suppress AID-mediated oncogenesis. We knocked down (KD) BRIP1 in the CH12F3-2A mouse B-cell, a model cell line for studying AID-induced physiological and non-physiological events and their underlying mechanisms. We also used biophysical assays and in silico tools to study non-B DNAs at human AID off-target sites. Here, we report that BRIP1 KD increased the frequency of AID-induced events, including IgM-to-IgA antibody switching, somatic hypermutation (SHM), DNA double-strand breaks (DSBs), and IgH/c-Myc chromosomal translocations. However, BRIP1 KD does not affect either the end-joining of AID-induced DNA breaks or the synapsis of switch regions. Importantly, BRIP1 KD resulted in the accumulation of R-loops at both AID targets and off-targets. Furthermore, in silico analysis revealed G4s as the most prevalent form of non-B DNA conformation at AID off-target sites in human. We propose that BRIP1 suppresses AID-induced genomic instability by resolving non-B DNA, thereby potentially limiting the accumulation of genomic lesions that contribute to B-cell lymphoma. These findings revealed that BRIP1 prevents the excessive accumulation of non-B DNAs at AID target sites and suppresses AID-mediated genomic instability. These data also provide a possible explanation for why BRIP1-deficient mice are predisposed to B-cell lymphoma.