Figure 3. Nucleosome occupancy and promoter states in the absence of Pho4p.

(a) Nucleosome occupancies for various amounts of basal ATPase activity designated as V_eff. The cyan curve is for V_eff = −7 k_BT with no sequence effects. Other curves are with sequence effects for V_eff = −10, −7, −4 and 0 k_BT values (top to bottom). The Pho4p binding sites, UAS1 and UAS2, and the TATA box are indicated by grey strips. (b) Promoter-state distribution: In the X-axis, the eight implicit promoter states are depicted schematically as boxes with nucleosomes as dots—the top dot is nucleosome N − 1 and the bottom dot is nucleosome N − 3. The Y-axis gives the probability of finding these states. CRB1 (circles) and CRB2 (squares) are experimentally measured probabilities of these promoter states when the PHO5 gene is repressed or inactive, as reported by Brown et al.⁴⁴ (for details, see text). The experimental findings are compared with our simulation results obtained under the same conditions as in (a). The inset indicates the average number of nucleosomes for various V_eff values. The region −8 < V_eff < −4 is shaded (grey) to indicate nucleosome density of ≈75% to 90%.