A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation
Fig 6
The effects of the initiation rate on the expression of adjacent genes.
(A) The construct for convergently, divergently, and codirectionally arranged genes where the initiation rate of one gene is varied (kmax = 0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2 s−1) and the initiation rate of the other gene is monitored in response to that of the first gene with an upper limit of kmax = 0.05 s−1. (B) The mean mRNA copy number of the monitored gene as a function of the maximum initiation rate (kmax) of the first gene, for the four constructs shown in (A). The dot is the mean and the shaded area is mean ± SEM. (C) The intergenic supercoiling density as a function the maximum initiation rate (kmax) of the adjacent gene. The dot is the mean and shaded area is mean ± SEM. (D) The empirical elongation rate of the monitored gene as a function of the maximum initiation rate (kmax) of the gene whose initiation rate is varied. The elongation rate is calculated for transcription events after 750 s, where the mean mRNA copy number already reaches a steady state (S14 Fig).