Figure 8. Simulations of RNA synthesis curve fitting to test the effects of different pausing percentages and residence times on our model.

(a,b) Different elongation speeds ranging from 1 to 5 kb min⁻¹ were simulated to illustrate that slower elongation speeds are inconsistent with our FRAP and photoactivation data. Data in a,b (black dots) are the same as in Figure 6j,t, respectively. (c) Best-fit solution predicts that a small fraction of polymerases (4.2% in our solution) enter long pauses; here we explored situations where different amounts of polymerases are forced to pause, ranging from 0% (dark blue) to 90% (green). A nonpausing system is simulated by a single-exponential fast decay, and increasing percentages of pausing allow the slow decay to dominate the simulation, gradually becoming the predominant population at the locus. This demonstrates that our model depends on only a small fraction of the polymerases pausing. Data (black dots) are the same as in Figure 6t. (d) Curves based on different pausing times illustrate that although our data (black dots; same as in Fig. 6t) cannot distinguish small differences in pausing time, larger variations are inconsistent with the data.