Cascades of Genetic Instability Resulting from Compromised Break-Induced Replication

Author Summary Maintaining genomic stability is important to prevent birth defects, genetic disorders and other diseases, including cancer. Double-strand DNA breaks (DSBs), which can result from exposure of living cells to ionizing radiation and various chemicals, threaten genomic integrity, thus making DSB repair essential. The choice of DSB repair pathway is important because some pathways confer destabilizing consequences. Break-induced replication (BIR) is a mechanism of DSB repair that is often associated with deleterious events that can threaten genetic stability. One such deleterious event is the formation of half-crossovers (HCs), which occurs when two chromosomes physically interacting during BIR repair fuse. Here we employed a yeast-based system to unravel the genetic factors promoting HC formation. We demonstrate that the interruption of BIR due to problems in DNA synthesis or checkpoint control, promote HCs. Additionally, we document that disruption of BIR promotes half-crossover-initiated cascades (HCC) that can significantly destabilize the genome and could be accounted as a potential mechanism responsible for cycles of non-reciprocal translocations contributing to cancer in humans. Break-induced replication (BIR) is a mechanism to repair double-strand breaks (DSBs) that possess only a single end that can find homology in the genome. This situation can result from the collapse of replication forks or telomere erosion. BIR frequently produces various genetic instabilities including mutations, loss of heterozygosity, deletions, duplications, and template switching that can result in copy-number variations (CNVs). An important type of genomic rearrangement specifically linked to BIR is half-crossovers (HCs), which result from fusions between parts of recombining chromosomes. Because HC formation produces a fused molecule as well as a broken chromosome fragment, these events could be highly destabilizing. Here we demonstrate that HC formation results from the interruption of BIR caused by a damaged template, defective replisome or premature onset of mitosis. Additionally, we document that checkpoint failure promotes channeling of BIR into half-crossover-initiated instability cascades (HCC) that resemble cycles of non-reciprocal translocations (NRTs) previously described in human tumors. We postulate that HCs represent a potent source of genetic destabilization with significant consequences that mimic those observed in human diseases, including cancer.