Abstract
Chromatin packages DNA inside eukaryotic nuclei, and the organization of chromatin governs the expression of packaged genes. Chromatin packaging confers latent adaptive epigenetic potential to cells. Pathogenic fungi and cancer can adapt to chemical threats or other adversities by restructuring chromatin accessibility to rewire gene expression. However, although we have many documented cases of chromatin remodeling in response to stress, we know very little about how this rapid and reversible adaptive strategy is implemented by cells over time. This complicates drug and treatment development when opposed with epigenetic transcriptional plasticity, necessitating understanding of this adaptive strategy in an ever-evolving arms race.Here, we construct a system devised to track the process of adaptive chromatin remodeling by using the model fission yeast, S.pombe, which redistributes the histone modification, H3K9 methylation (H3K9me), to repress gene expression to adapt to stress. Our unique precision-engineered system triggers population-wide epigenetic adaptation, revealing changes that lead to the formation of novel epigenetic adaptations over a five-day period. We show that, prior to adaptation, cells enter a slow-growth, stress response state. This is paired with the transient silencing of essential genes, which together form a state permissive for the nucleation of novel adaptive H3K9me.
Next, because epigenetic adaptations are reversible, we leveraged our system to remove stress to test reversibility and memory of adaptive H3K9me. We observed that, in previously adapted cells that were allowed to recover, adaptively silenced genes were quickly re-expressed. Upon reapplication of stress, there was a period of 6-8 cell divisions that allowed for the rapid return of adaptive H3K9me without reentry to the slow-growth state. By implementing genetic deletions that extend the retention of H3K9me, we are able to show that H3K9me is sufficient to retain adaptive memory in recovering cells. We uncouple H3K9me from adaptive gene silencing, which is possibly dependent on addition factors, including unique transcriptional states.
Lastly, we build from the foundation set by this work to further interrogate the mechanisms of adaptive H3K9me nucleation through a series of targeted deletions. These experiments serve to address several possible models for how cells nucleate novel adaptive H3K9me. We also expand our system to reduce the cost of future investigations using single-cell experiments to address questions of adaptive choice and rare sub-population formation. Overall, this work serves to set a foundation for constructing further understanding of adaptive epigenetic chromatin reorganization.