Ethanol stress induces siRNA-mediated epimutations and phenotypic variability in fission yeast

Abstract

Epigenetic information is required for the maintenance of gene expression states through cell division. Some epigenetic information can also persist through generations, raising the possibility that epigenetic differences may arise in populations and contribute to evolutionary processes such as drift and natural selection. Evaluating this requires characterising the properties of such epimutations, so that their rate, stability and genome-wide distribution can be assessed. Recent experiments in many organisms have demonstrated that epimutations occur, but have limited stability relative to DNA sequence mutations. However, the extent to which epimutations contribute to evolution is still unclear, in part because it is not clear whether epimutations respond dynamically to environmental conditions. Here, we use the fission yeast S. pombe, in which evolutionarily relevant epimutations have been observed, but not yet systematically characterised, to test whether a physiologically relevant stress, ethanol exposure, leads to changes in the properties of epimutations. Using laboratory evolution experiments with repeated population bottlenecks to minimise selection, we show that epimutations associated with changes in small interfering (si)RNAs occur at a greater rate in ethanol. Ethanol-induced epimutations are enriched at transposable element loci and correlate with changes in transposon expression. Ethanol exposure also increases gene expression noise genome-wide and variability in growth rate; importantly, both these increases are suppressed in mutants lacking siRNAs. Together, these results demonstrate that stress can alter the generation of heritable epigenetic information, and suggest that siRNAs may have a role in promoting phenotypic variability in response to environmental stress.