A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation
Fig 4
Dynamic topological domain formation results in bursty and noisy transcription from strong promoters through the accumulation and release of supercoiling.
(A-F) Comparison of a weak promoter (kmax = 0.005 s−1, top panel) and a strong promoter (kmax = 0.1 s−1, bottom panel) in their responses to supercoil density (A and D), mRNA copy number distribution when the DNA is open (unlooped, B and E) and when the DNA dynamically loops and unloops (C and F). (G-H) Exemplary mRNA production time traces (top panel) and the corresponding supercoil density of the DNA (bottom panel) for the strong promoter in the open-DNA condition (G) and the dynamically looping condition (H). The pink-shaded regions in H indicate the time when the loop is open. (I) Comparison of the Fano factor as a function of mean mRNA copy number for genes in an open DNA (blue) and that in a dynamically looping DNA condition (orange). The grey line denotes Fano factor = 1. (J) Comparison of the average initiation rate of genes when the DNA is open (green) and when the DNA is closed (red) in the dynamically looping DNA condition.