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. 2021 May 11;22:150. doi: 10.1186/s13059-021-02343-w

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 5 — Modeling and quantifying the effect of cohesin-dependent loops on chromatin structure in silico. a,b Chromosome structures and images generated by our multi-scale polymer simulation. The five images show example 3D super-resolution views of simulated chromosome regions, with (a) or without (b) loops. The genomic size of each region is indicated and ranges from 10 to 190 Mb. A snapshot of the simulated model is shown to the left. For animated 3D views, see Additional file 5: Video S4. c. Violin plots show the distribution of gyration radii and smoothness as function of loop counts per Mb or, equivalently, percentage of DNA enclosed by loops. Pink shading indicates where median values differ with intermediate significance (p < 0.05, light shade), or with high significance (p < 0.01, darker shade) from values in absence of loops (two-sided rank sum tests)