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. 2021 Aug 25;22:247. doi: 10.1186/s13059-021-02460-6

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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. 3 — Effect of TNF stimulation on the chromatin landscape in FLS. a Comparison of TADs boundaries between basal and TNF-stimulated FLS by TADCompare. Number of non-differential (green) and differential TAD boundaries is shown. Differential TAD boundaries are classified as boundary position changes (complex, merge, shifted, split) or strength change (differential boundary magnitude). Complex, merged, and split boundary changes represent the most disruptive changes of the 3D structure of the genome. b Pearson correlation of the loop intensity as determined by CHiC with change in the expression of nearby genes (log fold change). Negative numbers in the x-axis indicate downregulation, positive numbers upregulation of gene expression. c Graphical representation of the RNA-seq, ATAC-seq, and CHiC data integration to identify transcription factor binding sites in TNF-stimulated FLS. This figure was created using BioRender. d De novo DNA motif discovery identified two motifs (motif 2 and motif 3) with high similarity to the binding sites of homeobox (TAATTA) and forkhead box transcription factors (TAAA) in the dataset with TNF-repressed genes.