Genome instability footprint under rapamycin and hydroxyurea treatments

The mutational processes are jointly shaped by genetic backgrounds, environments and their interactions. Accurate quantification of mutation rates and spectra under drugs has important implications in disease treatment. Here, we used yeast mutation accumulation lines (MALs) to profile the genome-wide mutational footprints of two chemotherapy drugs across multiple genetic backgrounds. Together with time-resolved phenotyping, we investigated the mutagenic effects of rapamycin and hydroxyurea and the associated functional implications. In the absence of drug treatment, we observed genetic backgrounds variation in point mutation rates. In rapamycin, we observed comparable or lower mutation rates than in the untreated control. However, we identified frequent chromosome XII amplifications, which compensated for rapamycin induced rDNA repeat contraction on this chromosome and thereby served to maintain rDNA content homeostasis. In hydroxyurea, we detected pervasive mutation rate elevation independent of genetic backgrounds, with high occurrence of aneuploidy that associated with dramatic fitness loss. Hydroxyurea induced a high T-to-G transversion rate that reversed the common G/C-to-A/T bias in yeast, a broad range of structural variants and a mutation footprint consistent with mechanisms of error-prone polymerase activities and NHEJ repair pathways. Taken together, our study provides an in-depth view of mutation rates and signatures in rapamycin and hydroxyurea and their impact on cell fitness, which brings insights for assessing their long-term effects on genome integrity.