Despite its importance in transcriptional regulation, only recently has epigenetics attracted attention in the research of genomic expression variation and evolution. Recent studies suggested that positioned nucleosomes in a specific region of the promoter are associated with regulatory variation, regardless of being stochastic, environmental, genetic or evolutionary. Further, this intrinsically variable transcriptional pattern was proposed to be hardwired in the underlying promoter sequences that govern nucleosome organization. It seems that this nucleosome code for intrinsic variation is essential in the regulatory control of stress response. Stochastic remodeling of cis-encoded nucleosomes could provide transcriptional plasticity and resilience to transient environmental stresses. In response to long-term environmental challenges, however, genetic adaptation of the nucleosome code might lead to a converged epigenetic state, translating short-term adaptation into evolutionary adaptation. This is supported by the observation that the relevant nucleosome codes in the genomes of yeast species reflect their phylogenetic relationships.