Epigenetic gene silencing by heterochromatin primes fungal resistance

Sito Torres-Garcia, Pauline N. C. B. Audergon, Manu Shukla, Sharon A. White, Alison L. Pidoux, Robin C. Allshire

Preprint posted on 17 October 2019

Article now published in Nature at

Yeast chromatin high on caffeine! Torres-Garcia and colleagues describe a heritable heterochromatin-based response underlying resistance to moderate caffeine levels.

Selected by Miguel V. Almeida



Research on the fission yeast Schizosaccharomyces pombe has provided great insights into the process of heterochromatin formation. Clr4 is the only methyltransferase in S. pombe that deposits histone H3 lysine 9 methylation (H3K9me), often found in heterochromatic regions. Genes within H3K9me heterochromatin regions tend to be silenced.

Yeast cells are surprisingly recalcitrant to artificially-induced, heritable ectopic H3K9me heterochromatin. Indeed, in 2015 several labs described specific pathways actively blocking the transfer of spurious epigenetic information between generations. For example, the inactivation of the histone demethylase Epe1 allows transmission of ectopic heterochromatin across generations. Also, the strongly conserved RNA Polymerase-associated factor Paf1 inhibits the formation and transgenerational transmission of small RNA-driven heterochromatin. But this could not possibly be the whole story. Fission yeast researchers hypothesized that transmission of heterochromatin-based gene silencing may act in wild-type cells, under specific conditions. A new preprint from the Allshire laboratory reports on heritable heterochromatin-based gene silencing arising after exposure to an external insult – moderate caffeine levels.


Key findings

  • The authors designed and performed a screen to identify non-genetic epimutants displaying reversible resistance to moderate levels of caffeine. These isolates are termed epimutants because they lose caffeine resistance after a few generations growing without caffeine. Reversibility is key here, since genetic mutants were expected not to lose resistance over generations. The H3K9 methyltransferase Clr4 was required for resistance to caffeine, supporting a role of H3K9me in this process.
  • Ectopic H3K9me heterochromatin domains are present in isolates with reversible caffeine resistance, and the genes within these novel heterochromatin domains display reduced transcription levels.
  • Importantly, caffeine resistance was achieved by artificially tethering Clr4 to these genes, indicating that heterochromatin formation at these specific loci is sufficient to establish caffeine resistance.


What I like about this preprint?

While reading this article, the anecdotal reaction of Thomas Huxley when he was first told about natural selection came to mind: “How extremely stupid not to have thought of that!” I somehow have a feeling that the experimental approach behind these findings is intuitive. This preprint describes one strategy yeast cells evolved to integrate and respond to stressful environmental signals in a fast and reversible manner. This likely enables the cell population to successfully survive the perils of an ever-changing environment, without hard-wiring genetic change. Now, we have a mechanistic basis whereby heritable heterochromatin changes in specific genomic regions stimulate reversible stress resistance. The preprint was a nice read, and I really liked the Clr4 tethering-and-release experiments testing the sufficiency of heterochromatin formation in driving caffeine resistance.

One other aspect I like about this preprint is that it provides a guide on how to perform epigenetic screens. Classical genetic screens commonly employ very stringent parameters, and researchers tended to follow-up and characterize only the clear-cut mutants with the strongest expression of the phenotype of interest. This obviously ignored unstable, potentially reversible epimutants, which would be eliminated in subsequent screen validation. The work of Torres-Garcia and colleagues tells us to look also at the inherent instability of some screen hits. An important trick is to reduce stringency of the selection, like the moderate concentrations of caffeine used, instead of higher concentrations typically used in genetic screens.


Open questions

1) I wonder as to which factors initiate this response. Are normal sensors of stress directly informing H3K9 methyltransferases?

2) I find it intriguing that heterochromatin formation by Clr4 tethering to caffeine-resistance genes also leads to resistance to clotrimazole, a widely used clinical fungicide. Additionally, oxidative stress stimulated H3K9me2 deposition to the same caffeine-resistant loci, although to a lower extent. Therefore, this mechanism seems to be transversal to many different types of stresses. Why is that? And how does a population of yeast cells deal with simultaneous combinations of these stresses?

3) After removal of the insult, epimutants will revert back to the wild-type phenotype, while the genetic mutant will keep the mutant phenotype. At this point, is the plasticity of the (former) epimutant advantageous? In other words, after removal of the stress, is the genetic mutation costly in terms of fitness?

4) The authors finish by raising the issue of fungal resistance to fungicides. They propose the use of inhibitors of histone modifying enzymes in combination with conventional fungicides may preclude the onset of fungicide resistance. Such a development would be highly beneficial to many crops and animals, including immunocompromised humans, currently assailed by fungi. To determine the soundness of such strategies, it is important to first understand how widespread stress-induced heterochromatin-based responses are in fungi, especially pathogenic fungi.


Those issues remain to be determined. What we do know is, as corresponding author Robin Allshire tweeted: “Resistance is fungile!”


Want to know more?

Ten principles of heterochromatin formation and function, Allshire & Madhani, 2017.

Restricted epigenetic inheritance of H3K9 methylation, Audergon et al., 2015.

Epigenetic inheritance uncoupled from sequence-specific recruitment, Ragunathan et al., 2015.


Tags: caffeine resistance, epigenetic inheritance, fungi, heterochromatin, schizosaccharomyces pombe

Posted on: 14 November 2019


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