Genome instability footprint under rapamycin and hydroxyurea treatments

• The mutational processes dictating the accumulation of mutations in genomes are shaped by genetic background, environment and their interactions. Accurate quantification of mutation rates and spectra under drugs has important implications in disease treatment. Here, we used whole-genome sequencing and time-resolved growth phenotyping of yeast mutation accumulation lines to give a detailed view of the mutagenic effects of rapamycin and hydroxyurea on the genome and cell growth. Mutation rates depended on the genetic backgrounds but were only marginally affected by rapamycin. As a remarkable exception, rapamycin treatment was associated with frequent chromosome XII amplifications, which compensated for rapamycin induced rDNA repeat contraction on this chromosome and served to maintain rDNA content homeostasis and fitness. In hydroxyurea, a wide range of mutation rates were elevated regardless of the genetic backgrounds, with a particularly high occurrence of aneuploidy that associated with dramatic fitness loss. Hydroxyurea also induced a high T-to-G and low C-to-A transversion rate that reversed the common G/C-to-A/T bias in yeast and gave rise to a broad range of structural variants, including mtDNA deletions. The hydroxyurea mutation footprint was consistent with the activation of error-prone DNA polymerase activities and non-homologues end joining 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 chronic effects on genome integrity. As the ultimate source of genetic variation, mutation plays critical roles in evolution. An accurate depiction of its intrinsic rate and signature can help us understand the genetic basis of biodiversity and diseases. However, the ubiquitous existence of natural selection often leads to bias for the observable mutations in natural populations. To minimize such confounding effect introduced by selection, we applied evolution experiment by random single-cell bottlenecks, which allows almost all kinds of mutations to accumulate in an unbiased way. With this setup, we examined the mutation rates and signatures of yeast cells in two commonly used chemotherapy drugs that impairs essential cellular functions such as DNA and protein synthesis. We found elevated mutation rates for a wide range of genetic variants, accompanied by dramatic fitness loss in hydroxyurea. The mutational signatures suggest the involvement of low fidelity DNA replication and repair processes. The mutagenic effects of rapamycin are marginal but with frequent chromosome XII amplifications that compensate for rapamycin-induced rDNA contraction on this chromosome. Our findings provide an example of how such experiments on model organisms can help us better understand the chronic mutagenic effects of drugs and their underlying biological mechanisms.

Ämnesord

NATURVETENSKAP  -- Biologi -- Genetik (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Genetics (hsv//eng)

Publikations- och innehållstyp

ref (ämneskategori)

art (ämneskategori)