Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements

We explored how Cas9-induced double-strand breaks (DSBs) on Ty1 produce genomic alterations in the diploid yeast Saccharomyces cerevisiae. Following Cas9 induction, we observed a significant elevation of chromosome rearrangements (large deletions and duplications), loss of heterozygosity (gene conversions, crossovers, and break-induced replication), and aneuploidy. Almost all of the chromosomal rearrangements reflect the repairing of DSBs at Ty1 elements by homologous recombination. The goal of our experiments was to analyze genomic rearrangements induced in yeast by expression of a CRISPR/Cas9 system directed against a target in the repeated transposon Ty1. Using whole genome SNP microarrays, we analyzed genomic alterations in 18 yeast isolates. For each isolate, cells were under long-term or transient (2 hours or 4 hours) exposure of CRISPR/Cas9 for inducing double strand breaks on Ty1. MD741-3, -5, -6, -7 are from long-term exposure. We subcultured MD741-3, -5, -6, -7 for one time to analyze the ongoing instability. 2 colonies from each isolate were picked up for analyzing, named as MD741-3-S1, MD741-3-S2, MD741-5-S1, MD741-5-S2, MD741-6-S1, MD741-6-S2, MD741-7-S1, MD741-7-S2. MD704-2h-7, -26 are from 2 hours exposure. MD704-4h-1, -6P, -8, -12 are from 4 hours exposure.