Replication-Dependent Mechanism of Chromosome Fragility at the Site of Inverted Repeats in Saccharomyces cerevisiae

Genome instability is linked to cancer and many hereditary diseases. Chromosomal aberrations are often associated with repeats that can adopt DNA secondary structures. Studying the mechanism of genome instability caused by unstable motifs will therefore contribute to our understanding of the origin of human pathology. In this study, we investigate the mechanism underlying inverted repeated associated instability. A biological assay was used to identify mutant strains that showed increased instability in the presence of inverted repeats in the ∆sae2 or ∆mre11 background. Tetrad analysis techniques were used to map the mutations, and four mutations (all isolated independently) were identified in the CDC2 (POL3) gene. We focused on one mutation, pol3-6PL for this study. The effect of pol3-6PL on inverted repeat-mediated instability was assessed using armloss and gene amplification assays. Fluctuation tests on the mutant strain showed increased rates of these events. CHEF and Southern blot hybridization showed increased double-strand break formation at the site of inverted repeats. From this data, we propose a model for a replication-dependent mechanism of chromosomal fragility at the site of inverted repeats.