Epigenetic gene silencing by heterochromatin primes fungal resistance

Genes embedded in H3 lysine 9 methylation (H3K9me)–dependent heterochromatin are transcriptionally silenced(1–3). In fission yeast, Schizosaccharomyces pombe, H3K9me-mediated heterochromatin can be transmitted through cell division provided the counteracting demethylase Epe1 is absent(4,5). Under certain conditions wild-type cells might utilize heterochromatin heritability to form epimutations, phenotypes mediated by unstable silencing rather than DNA changes(6,7). Here we show that resistant heterochromatin-dependent epimutants arise in threshold levels of caffeine. Unstable resistant isolates exhibit distinct heterochromatin islands, which reduce expression of underlying genes, some of which confer resistance when mutated. Targeting synthetic heterochromatin to implicated loci confirms that resistance results from heterochromatin-mediated silencing. Our analyses reveal that epigenetic processes promote phenotypic plasticity, allowing wild-type cells to adapt to non-favorable environments without altering their genotype. In some isolates, subsequent or co-occurring gene amplification events augment resistance. Caffeine impacts two anti-silencing factors: Epe1 levels are downregulated, reducing its chromatin association; and Mst2 histone acetyltransferase expression switches to a shortened isoform. Thus, heterochromatin-dependent epimutant formation provides a bet-hedging strategy that allows cells to remain genetically wild-type but adapt transiently to external insults. Unstable caffeine-resistant isolates show cross-resistance to antifungal agents, suggesting that related heterochromatin-dependent processes may contribute to antifungal resistance in plant and human pathogenic fungi.