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. 2017 Nov 13;46(4):1648–1660. doi: 10.1093/nar/gkx1123

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© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — Consequences of limiting axial rotation of chromatin by cohesin handcuffs. (A–C) Modelling of TADs in which supercoiling can freely diffuse and be dissipated at TADs borders. (A) Starting, equilibrated configuration of modelled TAD with the active swivel ready for action and two sites where supercoiling can be dissipated. (B and C) two snapshots taken after 5 and 10 rotations of the active swivel, respectively. (D–F) Modelling of TADs in which free diffusion of supercoiling is strongly limited by cohesin handcuffs. (D) Starting, equilibrated configuration of modelled TAD, such as shown in A, but having in addition cohesin handcuffs placed between the active swivel and the TADs borders where supercoiling can be dissipated. (E and F) Two snapshots taken after 5 and 10 rotations of the active swivel, respectively. Notice accumulation of supercoiling in the chromatin portion between active swivels and cohesin handcuffs. Insets show ideograms and locations of active and passive swivels. Passive swivels are presented as sharp conical tips in contact with opposing surface. Torsional stress can freely dissipate by swivelling occurring at passive swivels. As mentioned in the legend to Figure 1, for better visualization of supercoiled regions chromatin fibres are shown with the diameter corresponding to 0.3σ instead of 1σ. However, the modelled cohesin handcuffs are presented with the diameter of 1σ, corresponding to the diameter they had during simulations.