Regulation of yeast PHO5 , adapted from Figures one and four b of [ ]. (A) Schematic of the experimental set-up. A doxycycline-inducible (Dox), YFP-tagged Pho4, modified to be constitutively active (SA1-4) and constitutively nuclear (PA6), stimulates expression of CFP from a partial PHO5 promoter, with three nucleosomes (-3, -2 and -1) and two Pho4 binding sites, a low-affinity exposed site between nucleosomes -2 and -3 (UASp1) and a high-affinity site occluded by nucleosome -2 (UASp2). The TATA box is occluded by nucleosome -1. (B) The labelled, directed graph of this system, showing the microstates (left) and the labels (bottom), in the notation used by Kim and O’Shea. Label a corresponds to Pho4 binding through a Hill function, which arises through the rapid equilibrium mechanism of Figure 3B. Labels b and c correspond to Pho4 unbinding (Figure 3C) from, respectively, UASp1 and UASp2. Labels d (k remod) and e (k reass) correspond to disassembly and assembly, respectively, of nucleosomes (Figure 3F), which introduce the non-equilibrium and irreversible features of the graph. Nucleosome -3 has been ignored in the graph. For other features, see the cited paper CFP, cyan fluorescent protein; YFP, yellow fluorescent protein.