Characterization of biased partner choice in mitotic non-allelic homologous recombination in Saccharomyces cerevisiae

We developed two diploid experimental systems in budding yeast, Saccharomyces cerevisiae, to study whether a strong deletion bias exists along the right arm of Chr 7. We have observed that Chr7R is frequently deleted as a recipient in translocations resulting from non-allelic homologous recombination. One system was used to study the effect of loss of heterozygosity (LOH) during mitotic recombination to determine whether Chr7 tends to break at one locus, indicating a possible fragile site, or if it breaks randomly along the right arm. To study this, we inserted a klURA3-ScURA3-KanMX4 CORE cassette, approximately 18 Kb from the telomere (TEL07R). 5-FOA resistant clones, clones that lost the LOH cassette, were chosen for whole genome sequencing. The other system placed a copy number variation (CNV) reporter system (SFA1-CUP1-KanMX4) approximately 24 Kb from the telomere (TEL07R) to investigate the behavior of Chr7R as a donor (rather than a recipient) in translocations. Sets of diploid clones possessing amplifications of the Chr7R CNV reporter cassette were isolated and whole genome sequenced. In addition to wild-type clones, knockouts for SWR1, SAE2, and SAP30 were included due to these genes having previously decreased the frequency of Chr7R acting as a translocation recipient when another chromosome arm was amplified. The broader characterization of Chr7's overactive behavior in genomic rearrangements will help us better understand the driving factors behind these large mutations, which are important contributors to developmental disorders and cancer.