Figure 1.

Active swivel that mimics a joint action of RNA polymerase with associated TOP1 introduces negative supercoiling into modelled chromatin fibre. (A) A snapshot of starting, thermally equilibrated configuration of a circular, coarse-grained chromatin fibre with the length corresponding to 120 kb and with one active swivel (shown in red). The active swivel is not working yet. (B and C) Snapshot of configurations obtained after the active swivel performed about 5 and 10 rotations, respectively. The inset shows ideograms of active swivels and indicates their locations. Segments of modelled chromatin fibre that flank the active swivel are forced to swivel with respect to each other. The direction of active swivelling is such that it introduces negative supercoiling, which results in formation of right-handed, interwound plectonemes. In all our figures, to visualize better the structure of plectonemically wound supercoiled regions, the chromatin fibres are shown with the diameter corresponding to 0.3σ instead of 1σ.