Epigenetic rewiring of cellular morphology and physiology in two Mendelian segregating traits associated with nutrient sensing

From prokaryotes to eukaryotes nutrient sensing plays a paramount role in living cells regulating cellular metabolism in response to sugars, amino acids, lipids and metabolites availability. Chromatin remodelling is emerging as an additional regulatory mechanism responding to nutritional sensing. The information on extracellular metabolites composition is transferred to the genome and “saved” at histone marks level leading to changes in metabolic pathways regulation. How and to which extent nutrients induce epigenetic modifications still remains elusive. In the present work we profiled histone acetylation and methylation as well as protein abundance levels in four meiotic individuals of a natural S. cerevisiae strain characterized by a Mendelian segregation of two nutrient-related traits: a recessive resistance to trifloroleucine (TFL) and a dominant filamentous morphotype. We found multiple histone mark modifications in regions associated with metabolic and transporter genes to segregate with the TFL-resistance trait as consequence of a loss-of-function mutation in the SSY1 amino acid sensor. Protein abundance variations in the same metabolic pathways pointed to a regulatory role of chromatin remodelling in response to environmental cues. We finally reported the association of facultative morphotypes with histone mark modifications identifying in the acetylation of NAB3 promoter a possible epigenetic hallmark of colony differentiation in response to nutritional stimuli.