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. 2023 Sep 12;14:5615. doi: 10.1038/s41467-023-41265-y

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© The Author(s) 2023

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 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/.

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Fig. 7 — a 1D model for stepwise and non-permanent blocking of Cohesin-mediated loop extrusion by clustered CBSs. Different lines describe the temporal progression of loop extrusion for four Cohesin complexes. Individual CBSs can block extruding complexes, but only in a non-permanent and possibly incomplete manner (exemplified by traffic lights). Isolated CBSs are unable to create long-term blocking of loop extrusion, resulting in weaker insulation between domains. Clustering of multiple CBSs, each inducing temporal blocking, promotes prolonged Cohesin residence at the boundary. Through the continuous influx of Cohesin, this increases the density of the Cohesin complex, thereby creating strong insulation. b A modified Randomly Cross-Linked (RCL) polymer model to simulate stepwise and non-permanent loop extrusion blocking at TAD boundaries. Top: scheme depicting the bead-spring chain with added boundary components. Blue monomers belong to TAD 1, orange monomers to TAD 2, blue/orange monomers can belong to either TAD and gray monomers belong to the gap without connectors. Connectors are placed at random positions within the same TAD (green lines) or fixed at the boundaries (red lines). Bottom: in silico Hi-C map of the 100 monomers that surround the (average) boundary. c Relative insulation score for the RCL model with different combinations of added boundary components. Numbers and color coding refer to the added boundary components from Fig. 7b. The black line represents the average insulation score at all boundaries in mESCs, as determined from reanalyzed Hi-C data. The gray line represents the original RCL model without any added boundary components¹⁰¹. Top: models with fixed connectors at the boundary; bottom: models without fixed connectors at the boundary. d Error estimates for the insulation score in the RCL model with different combinations of added boundary components, relative to experimental Hi-C data from mESCs (smaller values represent a smaller error). e An in silico RCL polymer model that incorporates all three aspects of dynamic and clustered CTCF binding results in an improved simulation of TAD boundary structure and function.