A transcriptional cycling model recapitulates chromatin-dependent features of noisy inducible transcription
Fig 2
The initial distribution of promoter states influences the heterogeneity in transcriptional activation modeled as an increase in PPRR.
(A) Three representative pie charts of fractional promoter-state probability of UP (blue), AP (teal) and BP (yellow) for BIR:BTR ratios of 0.1, 1, and 10 with PBR and PPRR held constant at 10 hr-1. Basal conditions were calculated from 1000 single-cell stochastic simulations out to 10 days for each parameter combination. At time = 0, PPRR was increased two-fold (B), and new fractional probabilities were captured at 2 hours. (B) Representative trajectories for BIR:BTR = 10 (pink), BIR:BTR = 1 (green), and BIR:BTR = 0.1 (cerulean). Each line represents one stochastic simulation out to 24 hours. Only 100 simulations are plotted for each condition for ease of visualization. Gray regions on the right represent the probability density of mRNA counts at 24 hours, with kernel smoothing. (C-D) Average mRNA counts (C) and Fano factor (D) for the three BIR:BTR ratios at 0, 1, 2, 4 and 24 hours. Average mRNA values and Fano factor were calculated from 1,000 single-cell stochastic simulation for each parameter combination. Error bars represent 95% bootstrapped confidence intervals. (E) Three representative pie charts of fractional promoter-state probability of UP (blue), AP (teal) and BP (yellow) for PPRR:PBR ratios of 0.1, 1, and 10 with BIR and BTR held constant at 0.1 hr-1. Fractional probabilities were calculated as described in (A). (F) Representative trajectories for PPRR:BBR = 0.1 (yellow), PPRR:PBR = 1 (green), and PPRR:PBR = 10 (orange). Data presented as described in (B). (G-H) Average mRNA counts (G) and Fano factor (H) for the three PPRR:PBR ratios at 0, 1, 2, 4 and 24 hours. Data presented as described in (C-D).