Figure 3.

Addition of a paused state to the model for transcription elongation. (A) Simulation of TEC movement from template position (i) to position (i + x), where the TEC may enter a paused state (Fig. S2), to position (i + n) (x = 10 and n = 20 for this simulation), under standard conditions as described for Fig. 1B above, with values for k_pausex and k_PEx of 10 and 0.1 nt s⁻¹, respectively. (Curves) Fraction of total TECs present at each sequential template position with time, beginning with template position (i) (black curve) and ending at position (i + 20) (light-blue curve), including the fraction of total TECs in the alternative paused state (dashed gray curve). (B) Comparison of TEC entry into template position (i + 19) in simulations with and without a paused alternative state at position (i + x) (dashed and solid curves, respectively), during the time-course of the simulation.