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Fig. 3 | Genome Biology

Fig. 3

From: 3D genome organization in the epithelial-mesenchymal transition spectrum

Fig. 3

a Definition of epithelial and mesenchymal TADs. b Top panel: Illustration of changes in EMT TADs between PEO1 (epithelial state) and HEYA8 (mesenchymal state), described by 4 categories: (i) Stable, (ii) Expand, (iii) Shrink, and (iv) Shift. The dashed lines represent the TAD boundaries that were identified in the cancer cell line, which was used as a reference of comparison. Bottom panel: Pie charts annotating the percentages of changes in HEYA8 eTADs with respect to PEO1 eTADs (left) and changes in PEO1 mTADs with respect to HEYA8 mTADs (right). c Distribution profile plots and heatmaps of the histones marks between PEO1 and HEYA8 in epithelial (left) and mesenchymal (right) TADs, split into the categories of TAD changes: (i) Stable, (ii) Expand, (iii) Shrink, and (iv) Shift. H3K4me1, H3K27ac, H3K27me3, and H3K9me3 are represented by indigo, green, black, and blue respectively. d Boxplots of normalized histones signal (y-axis; H3K4me1, H3K27ac, H3K27me3, and H3K9me3) in eTADs (top row) and mTADs (bottom row) of PEO1 (black) and HEYA8 (grey). The histones signals were split into the categories of TAD changes within each histone marks: (i) Stable, (ii) Expand, (iii) Shrink, and (iv) Shift. Student’s t test was carried out between PEO1 and HEYA8 for the respective histone marks, *p<0.05 **p<0.01, ***p<0.001 and ****p<0.0001. e Distribution profile plots and heatmaps of histone marks (H3K27ac—green, H3K27me3—black, and H3K9me3—blue) in eTADs (left) and mTADs (right) of cancer cell lines representing different states of the EMT spectrum. The relative epithelial and/or mesenchymal states of the cancer cell lines are shown as a color bar on top of the heatmaps (epithelial state—purple, mesenchymal state—orange). f Scatter plot showing Pearson correlation (R, x-axis) of EMT score to average histone signal in eTADs (purple circle) and mTADs (orange cross) across the cancer cell lines

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