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. 2022 Dec 5;54(12):1907–1918. doi: 10.1038/s41588-022-01232-7

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© The Author(s) 2022

Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a, Levels of agreement between simulations and experimental data as a function of loop extrusion parameters (here shown with extrusion speed 1 kb s⁻¹). The score represents the deviations of the distance, duration and fraction of time spent in the proximal state with those experimentally observed in the presence of RAD21 with or without 3 × CTCF sites (Methods). Magenta square, parameter set maximizing the agreement with experimental values. Yellow squares, four additional second-best parameter sets. b, Fraction of time spent in the proximal state called by HMM on simulations with the five best-matching parameters (magenta and yellow squares in panel a for +Extruder case, Methods). c, Average duration (mean ± 95% CI) of proximal state called by HMM on simulations with the five best-matching parameters. d, Fraction of time spent in the proximal state called by HMM on simulations (over n = 15,880 time points) for the best-matching parameter set in the presence of extruders (+) or low levels (−) of extruders, either with or without extrusion barriers. Shown are averages across experimental conditions; error bars represent bootstrapped (n = 10,000) standard deviations. e, Average duration of the proximal state (mean ± 95% CI, over n = 15,880 time points) either in the presence of extruders (+) or low levels of extruders (−), either with or without extrusion barriers. Two-sided Kolmogorov–Smirnov P values can be found in Supplementary Table 2. f, Representative trajectories of radial distances (gray), contact states called by HMM (full bar) and looped states in the underlying polymer conformations (striped bars) from +Extruders/+Barriers (top) and +Extruders/−Barriers simulations (bottom) with best-matching parameters (magenta square in panel a). g, Fraction of time spent in the looped state based on simulations with the five best-matching parameters. h, Average duration of the looped state based on simulations with the five best-matching parameters (mean ± 95% CI). i, Scheme summarizing the durations of proximal and looped states in the presence and absence of 3 × CTCF sites. a.u., arbitrary unit; sim, simulation.

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