Formation of chromosomal rearrangements in Saccharomyces cerevisiae diploids through regionally-biased non-allelic homologous recombination

In earlier studies, we optimized an assay system for the genome-wide detection of copy number variation (CNV) in diploid Saccharomyces cerevisiae cells, based on selection for formaldehyde plus copper (FA+Cu) resistance conferred by the amplification of a dosage-dependent reporter cassette, SFA1-CUP1. Our analyses identified a robust bias for terminal deletions of the right arm of Chr7 (Chr7R) associated with unbalanced translocations. This bias was observed at approximately constant strength across all three sites where the amplification reporter cassette was inserted, in CNV-carrying yeast clones derived both spontaneously and from mutagen-induced recombinogenic conditions. We conducted allelic mitotic recombination experiments to investigate the possibility of the presence of a fragile site on Chr7R, but the results disfavored this model, and instead indicated that the Chr7R bias applies only to non-allelic rearrangements. We validated the existence of a CNV formation bias at Chr7R through an orthologous NAHR competition approach that was independent of selection for FA+Cu resistance. Finally, we showed the in contrast to its high participation in NAHR as a recipient sequence, Chr7R becomes amplified as a translocation donor less frequently than other comparable regions of the genome. To begin unraveling the cause of this unusual behavior, we evaluated the effect of a set of candidate genes involved in chromatin mobility and sister chromatid cohesion on the rearrangement spectra involving Chr7R. We found that deletion mutations in some of these genes, particularly SAP30, attenuated the biased NAHR behavior. Taken together, our results suggested that although Chr7R is not inherently more prone to DNA breakage than other regions, once a DNA lesion is formed there, it has a higher propensity to undergo inappropriate repair leading to a chromosomal rearrangement.