Fig. 2.

Nucleosome dynamics away from, but not in, equilibrium allow for increased activator fidelity and attenuation of transcription noise. (A) Transition graph of Model 2. (B) Activator fidelity of Model 2 $\left(f_2\right)$ normalized by the fidelity of Model 1 $\left(f_1\right)$, as a function of the rate of nucleosome removal in the activator-bound state, $\alpha$, normalized by the rate of removal in the unbound state, $\lambda$. For calculations, we assumed $\kappa =1$, $k_C=1$, $k_i=100$, $\beta =2$, and $\lambda =0.1$. The gray dot indicates the equilibrium state. (C) Representative sample paths at relative activator fidelity $f_2/f_0=0.95$ and $v_C=5$ for nonequilibrium nucleosome dynamics (dark gray; $\alpha =2$, $\lambda =0.1$), which required $\kappa =4.26$ and $\mu =13.26$; and equilibrium dynamics (light gray; $\alpha ,\lambda =2$), which required $\kappa =0.053$ and $\mu =198.68$. For both simulations, we assumed $\delta =0.1$. (D) Transcription noise as a function of relative activator fidelity, $f\left(\kappa ,\mu \right)/f_0$, for Model 2 in equilibrium (light gray, 2 [α = λ]; α, λ = 2), away from equilibrium (blue, 2 [α > λ]; $\alpha =2$, $\lambda =0.1$), and Model 1 (dashed line, 1; same as in Fig. 1D). For all calculations, we assumed, as above, $k_C=1$, $\delta =0.1$, and $v_C=5$. Fano factor and activator fidelity were calculated as functions of the activator on-rate, κ, and the rate of transcription in the active state, $\mu$ (SI Appendix). (E) Entropy production (in units of $k_B$, the Boltzmann constant) as a function of nucleosome removal rate in the activator-bound state, $\alpha$, relative to the rate in the unbound state, $\lambda =0.1$, for $\kappa =1$, $k_C=1$, and $\beta =2$. The gray dot indicates the equilibrium state.