Single-cell analysis of aneuploidy events using yeast whole chromosome painting probes (WCPPs)

• A panel of whole yeast chromosome painting probes (WCPPs) was constructed.
• Aneuploidy promoting conditions were revealed.
• Aberrant epigenetic regulation may contribute to genomic instability.
• A ranking of the most aneuploidy prone chromosomes was created.
• WCPPs are molecular tools for monitoring aneuploidy at the single-cell level.

Aneuploidy is considered a widespread genetic variation in such cell populations as yeast strains, cell lines and cancer cells, and spontaneous changes in the chromosomal copy number may have implications for data interpretation. Thus, aneuploidy monitoring is essential during routine laboratory practice, especially while conducting biochemical and/or gene expression analyses. In the present study, we constructed a panel of whole chromosome painting probes (WCPPs) to monitor aneuploidy in a single yeast Saccharomyces cerevisiae cell. The WCPP-based system was validated using “normal” haploid and diploid cells, as well as disomic cells both with and without cell synchronisation. FISH that utilised WCPPs was combined with DNA cell cycle analysis (imaging cytometry) to provide a detailed analysis of signal variability during the cell cycle. Chromosome painting can be utilised to detect spontaneously formed disomic chromosomes and study aneuploidy-promoting conditions. For example, the frequency of disomic chromosomes was increased in cells lacking NAD+-dependent histone deacetylase Sir2p compared with wild-type cells (p < 0.05). In conclusion, WCPPs may be considered to be a powerful molecular tool to identify individual genomic differences. Moreover, the WCPP-based system may be used at the single-cell level of analysis to supplement array-based techniques and high-throughput analyses at the population scale.