Figure 7.
Two modes of TF occupancy within a nucleosome entry–exit region. Top row: For binding sites contained within the first 30 bp of the nucleosome, k21/k23 is much larger than the dissociation constant, KD. For P26 nucleosomes, the KD value on a plot of [Gal4]/(k21/k23) versus [Gal4] (orange line) is significantly below 1, which is the Gal4 concentration that equals k21/k23 (red dashed line). As Gal4 significantly occupies its binding site at concentrations around the KD, (i) the binding mechanism continues to involve the nucleosome undergoing many unwrapping/rewrapping fluctuations before a Gal4 binding event traps the nucleosome in an unwrapped state, and (ii) the dissociation mechanism results in most Gal4 dissociation events being followed by nucleosome rewrapping. Bottom row: For binding sites that extend >30 bp into the nucleosome, k21/k23 is similar to the dissociation constant, KD. For P31 and P36 nucleosomes, the KD value on a plot of [Gal4]/(k21/k23) versus [Gal4] (green and magenta lines, respectively) is close to 1, which is the Gal4 concentration that equals k21/k23 (red dashed line). As Gal4 significantly occupies its binding site at concentrations around the KD, (i) the binding mechanism is limited by the nucleosome unwrapping rate, so Gal4 binds its site after each unwrapping event, and (ii) the dissociation mechanism results in multiple Gal4 dissociation and rebinding events before the nucleosome unwraps. Error indicates ±1 SD from single-molecule measurement of k21/k23.