Alterations to the yeast chromatin landscape during hypoxia

When cells encounter low oxygen conditions, signaling events target key transcription factors to reprogram gene expression to promote cell survival and adaptation under this challenging environmental stress. The substantial metabolic changes that occur in hypoxia also drive changes to the chromatin environment due to altered cofactor availability and direct oxygen sensitivity of chromatin-modifying enzymes, among other factors. Given the links between hypoxic cellular environments and numerous pathophysiological processes, including tumor progression and metastasis, cardiovascular disorders, and aberrant development, it is critical to understand the chromatin states and chromatin-based regulatory mechanisms associated with cellular responses to hypoxia. Here, we used the model eukaryote Saccharomyces cerevisiae to interrogate the requirement for key transcription factors and chromatin regulators in survival during hypoxia and we assessed the distribution of major histone modifications associated with the response to stress, H3K9 acetylation and H3K4 methylation, throughout the genome during hypoxia. Our results show that only a small number of chromatin modifiers in yeast contribute to survival in hypoxia; however, there are substantial changes to the abundance and distribution of both H3K9ac and H3K4me3 during hypoxic growth. Specifically, H3K9ac levels are reduced throughout the genome though still maintain association with transcriptionally active genes. H3K4me3 has increased abundance genome-wide and shows a wider distribution with greater abundance in coding sequences particularly of genes upregulated in hypoxic conditions. Altogether, our data demonstrate substantial changes to the chromatin landscape in hypoxic conditions in the budding yeast model, providing key insights into physiological chromatin changes caused by limiting oxygen in the environment.