A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation
Fig 3
Cooperation holds under the condition of fast Topo I unbinding and moderate supercoiling diffusion.
(A to C) Examples of the elongation rate–initiation rate curves (blue dots) and the corresponding piecewise linear fitting (red lines) for three different combinations of the Topo I unbinding rate and supercoil diffusion rate. Fitting is only performed for scenarios where the maximum empirical initiation rate is greater than 0.05 s−1 (i.e., C is not fitted). The fitted slope (k) values and fitting goodness (r2) were displayed in the legend. Grey stars correspond to the experimental data in Kim et al. [13]. (D) Heatmap of RNAP cooperativity, characterized by the slope of the elongation rate–initiation rate curve, under different supercoiling diffusion coefficients and Topo I unbinding rates. The grey region corresponds to the regime where the fitting goodness r2 is below 0.85, or the fitting is not performed (maximum initiation rate < 0.05 s−1). The red star indicates parameters used in the rest of the paper. (E) Heatmap of the mean squared error (MSE) between the model and the experimental data from Kim et al. [13].