Epigenetic gene silencing by heterochromatin primes fungal resistance

Genes embedded in H3 lysine 9 methylation (H3K9me)-dependent heterochromatin are transcriptionally silenced. In fission yeast, Schizosaccharomyces pombe, H3K9me heterochromatin silencing can be transmitted through cell division provided the counteracting demethylase Epe1 is absent. It is possible that under certain conditions wild-type cells might utilize heterochromatin heritability to form epimutations, phenotypes mediated by unstable silencing rather than changes in DNA. Here we show that resistant heterochromatin-mediated epimutants are formed in response to threshold levels of the external insult caffeine. ChIP-seq analyses of unstable resistant isolates revealed new distinct heterochromatin domains, which in some cases reduce the expression of underlying genes that are known to confer resistance when deleted. Targeting synthetic heterochromatin at implicated loci confirmed that resistance results from heterochromatin-mediated silencing. Our analyses reveal that epigenetic processes allow wild-type fission yeast to adapt to non-favorable environments without altering their genotype. In some isolates, subsequent or co-occurring gene amplification events enhance resistance. Thus, heterochromatin-dependent epimutant formation provides a bet-hedging strategy that allows cells to remain genetically wild-type but transiently adapt to external insults. As unstable caffeine-resistant isolates show cross-resistance to the fungicide clotrimazole it is likely that related heterochromatin-dependent processes contribute to anti-fungal resistance in both plant and human pathogenic fungi.