Figure 5. Loss of nucleosomes allows Rap1 to bind to intermediate-affinity targets.

A) Nucleosome occupancy was determined by ChIP-chip with an anti-Histone H3 antibody during exponential growth in the presence of glucose (left) and after glucose had been depleted from the media (right). Nucleosome occupancy is plotted relative to static targets during exponential growth. Error bars indicate the standard error. During growth in the presence of glucose, unbound low-glucose targets have a higher nucleosome occupancy then bound-static targets (p = 0.073). In the absence of glucose, both groups of targets are bound by Rap1, but low-glucose sites have significantly lower (p < 5 × 10⁻⁵) nucleosome occupancy than static targets. Experiment numbers are indicated in parentheses. B) Loci were sorted by their change in nucleosome occupancy upon glucose depletion. A moving average of the change in Rap1 occupancy upon glucose depletion is plotted on the y-axis. C) Intergenic regions were grouped into three categories based on their Rap1 binding affinity (high, intermediate, or low affinity) as measured by PBM²⁹. The 306 high-affinity regions had PBM p-values less than 1 × 10⁻⁶, the 288 intermediate affinity regions had PBM p-values between 0.01 and 1 × 10⁻⁶, and the remaining 4945 sites were classified as low-affinity. The average change in Rap1 occupancy (x axis) was determined for each group as a function of the change in nucleosome occupancy (y axis). D) Low-glucose Rap1 targets are on a nucleosomal hair-trigger. Nucleosome occupancy in the presence (black) and absence (gray) of glucose is plotted for all yeast intergenic regions. Values are relative to static Rap1 targets in the presence of glucose. Intergenic regions were separated into five groups: static Rap1 targets, low-glucose Rap1 targets, unbound loci containing high-affinity Rap1 sites, unbound loci containing intermediate-affinity Rap1 sites and unbound loci containing low-affinity Rap1 sites.