Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts
Fig 6
Evaluation of the effects of gene length and nucleosome spacing on bulk transcriptional properties.
Panels A (v), B (ρ), and C (J) show the results of a parameter sweep with respect to gene length from 2,000 to 20,000 bp with α = 0.1 (top left), 0.25 (top right), 0.5 (bottom left), and 1 (bottom right), and γ = 0.1 (blue), 0.2, (green), 0.4 (orange), and 0.75 (red). Panels D (v), E (ρ), and F (J) show the results of a parameter sweep with respect to the number of evenly spaced nucleosomes (by varying number of linker sites) giving NNuc∈{1, 4, 8, 16, 20, 25, 40, 50, 80, 100} with α = 0.1 (top left), 0.25 (top right), 0.5 (bottom left), and 1 (bottom right). Since γ depends on geometry, ho and hc were set equal to 1 (blue), 0.1 (green), and 0.01 (orange). Both sweeps were performed with 2×106 Monte Carlo steps and 50 replicates.