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. 2023 Nov 4;13:19085. doi: 10.1038/s41598-023-46415-2

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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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Transcription factor binding sites correlate with variations in the co-expression of tTRE Hi-C contacts. (a) Intersection by an insulator is associated with decreased Hi-C contact frequency. Top: Diagram of the intersecting CTCF binding site. Bottom: Distributions of Hi-C contact frequencies for tTRE pairs intersected by 2 or more CTCF sites and 1 or less, binned by distance. (b) Coactivator occupancy is associated with increased Hi-C contact frequency. Top: Diagram of P300 occupancy of a tTRE. Bottom: Hi-C contact frequencies for tTRE pairs occupied and unoccupied by P300, binned by distance. (c) “Bivalent” association of RAD21 with Hi-C contact frequency depending on tTRE intersection or occupancy. Left: Hi-C contact frequency distributions for tTRE pairs intersected by two or more RAD21 sites and one or less, binned by distances. Hi-C contact frequencies for tTRE pairs occupied or not occupied by RAD21, binned by distances. (d) Scatterplot of TF-dependent ∆AUCs comparing PRO-cap coexpression and Hi-C contacts. Each dot represents a TF, and selected TFs are highlighted. Left: ∆AUC scatterplot of TF overlap. Right: ∆AUC scatterplot of TF occupancy. The number of tTRE pairs in each distance bins in panels (a–c) are indicated in Supplementary Table 3.