DNA nicks induce mutational signatures associated with BRCA1 deficiency

Analysis of human cancer genome sequences has revealed specificmutational signatures associated with BRCA1-deficient tumors, but the underlying mechanisms remain poorly understood. Here, we show that one-ended DNA double strand breaks (DSBs) converted from CRISPR/Cas9-induced nicks by DNAreplication, not two-ended DSBs, cause more characteristic chromosomal aberrations and micronuclei in Brca1-deficient cells than in wild-type cells. BRCA1 is required for efficient homologous recombination of these nickconverted DSBs and suppresses bias towards long tract gene conversion and tandem duplication (TD) mediated by two-round strand invasion in a replication strand asymmetry. However, aberrant repair of these nick-converted one-endedDSBs, not that of two-endedDSBs inBrca1-deficient cells, generates mutational signatures such as small indels with microhomology (MH) at the junctions, translocations and small MH-mediated TDs, resembling those in BRCA1-deficient tumors. These results suggest a major contribution of DNA nicks tomutational signatures associated with BRCA1 deficiency in cancer and the underlying mechanisms.

Automated summary

Analysis of human cancer genome sequences has identified specific mutation characteristics associated with BRCA1-deficient tumors, but the mechanisms behind them are not well understood. In this study, it was found that one-ended DNA double strand breaks (DSBs) converted from CRISPR/Cas9-induced nicks by DNA replication, rather than two-ended DSBs, cause more chromosomal aberrations and micronuclei in Brca1-deficient cells. BRCA1 is required for efficient homologous recombination of these nick-converted DSBs and suppresses bias towards long tract gene conversion and tandem duplication mediated by two-round strand invasion in a replication strand asymmetry. However, abnormal repair of these nick-converted one-ended DSBs, not of two-ended DSBs in Brca1-deficient cells, generates mutational signatures similar to those observed in BRCA1-deficient tumors. These results suggest that DNA nicks play a major role in the mutational signatures associated with BRCA1 deficiency in cancer and shed light on the underlying mechanisms.