Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts
Fig 4
The ddTASEP phase diagram in the αγ-plane.
(A) Phase diagram in the αγ-plane (orthogonal to the original αß-plane in Fig 1B at ß = q = 1). The critical line (Eq 37) divides the phase diagram into two regions: the initiation-limited and the nucleosome-limited For γ→1, the ddTASEP’s dynamics converge to the classical Max Flux Limit shown in Fig 1B. (B) The theoretical predictions (top row) for the bulk elongation rate v (Eq 38), bulk density ρ (Eq 39), and bulk transcription flux J (Eq 40) are qualitatively compared to simulated results for hc = 0.1, 0.01, and 0.001 (2nd through 4th rows) Mean first passage rate, γ was varied from between 0 and 1 by specifying hc (for given ho) to achieve the desired value. 1.2 million simulation steps were used for each heat map point.