Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt

Fungal survival in harsh environments involves stress-sensing pathways that reprogram their
proteomes. New conditions, including climate change, can push opportunistic fungi to colonise
novel niches, potentially becoming harmful pathogens. Effective antifungal/fungicide treatments
are limited in number precisely because fungi are adept at resisting challenges. Antifungal
resistance is increasingly prevalent, raising fungal-borne disease frequencies in humans and
crops1. Conventional wisdom that resistance results solely from genetic mutations was
overturned by our discovery that external insults selects for cells with a distinct epigenetic
landscape - repressive heterochromatin over various genes whose reduced expression confers
resistance (e.g. mitochondrial proteins)2,3. Such heterochromatin-dependent ‘epimutations’ are
unstable, slowly losing resistance upon external insult removal. We hypothesize that extracellular
stresses, including fungicides widely used in agriculture, reprogramme fungal epigenomes so that
they transiently acquire heterochromatin at locations which confer heritable, but unstable,
resistance. By employing single cell analysis of lineages seeded by just one cell we aim to provide
insight into the mechanisms utilized by cells to mediate epimutant-mediated resistance. This
project will combine the power of classic Luria-Delbruck fluctuation tests with low cell
number/single cell (ATAC-seq, Cut&Tag and RNA-seq) sequencing workflows to dissect the events
that result in the emergence of transiently antifungal/fungicide resistant lineages due to
epimutation formation.

Relevant literature

1. Fisher MC, Hawkins NJ, Sanglard D. & Gurr SJ. (2018) Worldwide emergence of resistance to
antifungal drugs challenges human health and food security. Science 360, 739–742

2. Torres-Garcia S, Yaseen I, Shukla M, Audergon PNCB, White SA, Pidoux AL, Allshire RC.
(2020). Epigenetic gene silencing by heterochromatin primes fungal resistance. Nature 585,

3. Yaseen I, White SA, Torres-Garcia S, Spanos C, Lafos M, Gaberdiel E, Yeboah R, El Karoui M,
Rappsilber J, Pidoux AL, Allshire RC. (2022) Proteasome-dependent truncation of the
negative heterochromatin regulator Epe1 mediates antifungal resistance. Nature Structure
& Molecular Biology (in press); BioRXiv: doi.org/10.1101/2021.12.20.473483

4. A. Danese, M.L. Richter, D.S. Fischer, F.J. Theis and M. Colomé-Tatché. EpiScanpy:
integrated single-cell epigenomic analysis. Nat. Commun. 12, 5228 (2021).

5. A. vd Graaf, R. Wardenaar, D.A. Neumann, A. Taudt, R.G. Shaw, R.C. Jansen, R.J. Schmitz*,
M. Colomé-Tatché*, F. Johannes*. Rate, spectrum and evolutionary dynamics of
spontaneous epimutations. Proc. Natl. Acad. Sci. USA 112:6676-81 (2015). (* cocorresponding