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. 2019 Oct 24;10:4843. doi: 10.1038/s41467-019-12811-4

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© The Author(s) 2019

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. 4 — Changes in TAD boundaries and intra-TAD interactions. a Boundary alterations in NSD2 High versus Low cells. NSD2 overexpression is associated with increases (red, 61) and decreases (blue, 5) in TAD boundary strength (n = 2 independent experiments, cutoffs of absolute Log2-fold change > 0.1 and FDR < 0.05). b TAD boundary increases and decreases in NSD2 High versus Low cells are associated with increases and decreases in CTCF and Rad21 binding, respectively. The median is indicated under the violins. c Intra-TAD interaction changes in NSD2 High versus Low cells for overlapping TADs (1564). NSD2 overexpression is associated with gain (red, 229) and loss (blue, 30) of intra-TAD interactions (n = 2 independent experiments, cutoffs of absolute Log2-fold change > 0.3 and FDR < 0.05). d Changes in H3K36me2 and H3K27me3 within TADs that have increased (red), decreased (red), or stable (gray) interactions in NSD2 High cells. Log2-Fold changes (NSD2 High/Low cells) for H3K36me2 and H3K27me3 ChIP-seq are shown. The median is indicated under the violins. e UCSC tracks showing chromatin features in the region surrounding the FZD8 gene (FZD8 gene indicated in red and location highlighted by a yellow stripe) and the new contact that is formed by a strengthened boundary (blue stripe). The graphical representation of interaction between FZD8 and the super enhancer is shown as a loop below. H–L refers to subtraction of the ChIP-seq signal (NSD2 High–Low). f Hi-C plots of the region surrounding the FZD8 gene. Top panel: NSD2 Low, bottom panel: NSD2 High. Green arrow identifies the TAD boundary that is strengthened in NSD2 High versus Low cells. Black arrow indicates the FZD8 gene. Circle indicates a new loop between FZD8 and the boundary. Source data for violin plots in panels b and d are provided as a Source Data file