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. 2017 Aug 11;45(17):9850–9859. doi: 10.1093/nar/gkx716

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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 1. — Simulations of effects of divergent transcription in a small chromatin loop in which positive supercoiling generated ahead of RNA polymerases is dissipated. (A–C) Simulation snapshots showing gradual accumulation of negative supercoiling. The starting configuration is shown in A. The arrowhead-shaped objects indicate positions of torsional motors that mimic the effect of RNA polymerases by generating torque and inducing local axial rotation of the chain. The modelled chain reflects the properties of semi-flexible polymers like DNA or chromatin fibres with bending and torsional resistance. Only in the short region between the two torsional motors the chain has no torsional resistance. The region with no torsional resistance (swivel) is graphically presented as a sharp tip contacting a flat surface to resemble a tip of a spinning top that is in a contact with the supporting surface but is free to rotate. (D) The magnitude of writhe (one of the measures of supercoiling (32)) increases and then saturates with time (the writhe in negatively supercoiled DNA and chromatin fibres is negative).