Single-Gene Deletions Contributing to Loss of Heterozygosity in Saccharomyces cerevisiae: Genome-Wide Screens and Reproducibility

Abstract

Abstract Loss of heterozygosity (LOH) is a phenomenon commonly observed in cancers; the loss of chromosomal regions can be both causal and indicative of underlying genome instability. Yeast has long been used as a model organism to study genetic mechanisms difficult to study in mammalian cells. Studying gene deletions leading to increased LOH in yeast aids our understanding of the processes involved, and guides exploration into the etiology of LOH in cancers. Yet, before in-depth mechanistic studies can occur, candidate genes of interest must be identified. Utilizing the heterozygous Saccharomyces cerevisiae deletion collection (≈ 6500 strains), 217 genes whose disruption leads to increased LOH events at the endogenously heterozygous mating type locus were identified. Our investigation to refine this list of genes to candidates with the most definite impact on LOH includes: secondary testing for LOH impact at an additional locus, gene ontology analysis to determine common gene characteristics, and positional gene enrichment studies to identify chromosomal regions important in LOH events. Further, we conducted extensive comparisons of our data to screens with similar, but distinct methodologies, to further distinguish genes that are more likely to be true contributors to instability due to their reproducibility, and not just identified due to the stochastic nature of LOH. Finally, we selected nine candidate genes and quantitatively measured their impact on LOH as a benchmark for the impact of genes identified in our study. Our data add to the existing body of work and strengthen the evidence of single-gene knockdowns contributing to genome instability.