Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts
Fig 7
Investigation of the ddTASEP Inter-Burst Interval and Average Burst Size.
(A) Representative smoothed kernel density estimates of log10(tw) weighted by log10(tw) using same parameter sets as Fig 2. (B) Empirical cumulative distribution functions of waiting times (black line) from ddTASEPs with the same parameters as in Fig 2. The time-headway cumulative distribution function is overlaid for each plot (Eq 42). The red dashed time headway distributions have robust bursting with an effective density ρeff = 0.5. In contrast, the green dashed lines indicate initiation limited cases where unimodality was observed in Fig 7A, and ρ is given by Eq 39. (C) shows the average inter-burst interval plotted as a function of Eh = 4/γ. (D) shows the average inter-burst interval
plotted as a function of index of dispersion of the first passage time to enter a nucleosome De. (E) shows burst size
plotted as a function of mean first passage rate γ with the solid lines proportional to
. Panels (C), (D), and (E) were generated with Fig 5A–5C. γ is varied from 0.001 to 0.99 by adjusting ho for fixed values of hc equal to 0.001 (blue), 0.01 (green), and 0.1 (orange) omitting cases that failed to show bimodality.