Fig. 4

a Aggregate TAD plot showing normalized observed/expected Hi-C counts in the eTADs (top row) and mTADs (bottom row) of cancer cell lines—PEO1 (purple), A549 (white), and HEYA8 (orange)—arranged in the order of increasing EMT score (from epithelial to mesenchymal state). Boxplot representations of the observed/expected Hi-C counts (y-axis) within the eTADs or mTADs of the cancer cell lines (x-axis) are depicted on the right of the aggregate TAD plots. Student’s t test was used for the statistical analysis, ****p < 0.0001. b Aggregate Hi-C matrices showing the interaction z-scores (red: high interaction z-score, blue: low interaction z-score) at pairwise genomic regions, between TSS of epithelial genes to the other genes within the eTADs of cancer cell lines—PEO1 (purple), A549 (white), and HEYA8 (orange)—arranged in the order of increasing EMT score (from epithelial to mesenchymal state). Distribution profile plots of the histone marks (H3K27ac—green, H3K27me3—black, and H3K4me1—indigo) at the TSS of epithelial genes were shown below the respective aggregate Hi-C matrices. Boxplot representation of interaction z-scores, as highlighted by the dashed boxes in the aggregate matrices, (y-axis) at the TSS of epithelial genes across the cancer cell lines (x-axis) of different EMT scores along the EMT spectrum. Student’s t test was used for the statistical analysis. c Aggregate Hi-C matrices showing the interaction z-scores (red: high interaction z-score, blue: low interaction z-score) at pairwise genomic regions, between TSS of mesenchymal genes to the other genes within the mTADs of cancer cell lines—PEO1 (purple), A549 (white), and HEYA8 (orange)—arranged in the order of increasing EMT score (from epithelial to mesenchymal state). Distribution profile plots of the histone marks (H3K27ac—green, H3K27me3—black, and H3K4me1—indigo) at the TSS of mesenchymal genes were shown below the respective aggregate Hi-C matrices. Boxplot representation of interaction z-scores, as highlighted by the dashed boxes in the aggregate matrices, (y-axis) at the TSS of mesenchymal genes across the cancer cell lines (x-axis) of different EMT scores along the EMT spectrum. Student’s t test was used for the statistical analysis, **p< 0.01, ***p<0.001 and ****p<0.0001. d Triangular Hi-C matrix showing the normalized Hi-C counts at CDH1 and CDH2 TADs (chr16:68,300,000–68,900,000 and chr18:27,600,000–28,250,000, respectively) in PEO1 (top Hi-C matrix) and HEYA8 (bottom inverted Hi-C matrix). The TADs at CDH1 and CDH2 loci are represented by the solid black lines drawn on the Hi-C matrix. Histone marks in the 4 ovarian cancer cell lines (PEO1, OVCA429, SKOV3, and HEYA8) are shown below the Hi-C matrices. H3K4me1, H3K27ac, and H3K27me3 are represented by indigo, green, and black respectively. The gene track (hg38) is shown below the histone marks tracks. The dotted arcs, below the gene track, represent the interacting loci that were used in assessing the interaction frequency by 3C-qPCR. The interacting loci were also annotated in the triangular Hi-C matrices by the grey arrows. e Bar chart representation of 3C-qPCR interaction frequencies (y-axis) between interacting loci (x-axis) annotated in d, in 4 ovarian cancer cell lines (PEO1, OVCA429, SKOV3, and HEYA8). The interacting loci assessed by 3C-qPCR at the CDH1 TAD are “CDH1-CDH3” (CDH1 TSS to CDH3 TSS), “CDH3-ZFP90” (CDH3 TSS to ZFP90 TSS), “CDH1- ZFP90” (CDH1 TSS to ZFP90 TSS), and “CDH1 TAD boundary” (CDH1 TAD 5′boundary to 3′boundary). The interacting loci assessed by 3C-qPCR at the CDH2 TAD are “CDH2 TSS-intron” (CDH2 TSS to CDH2 intronic enhancer), “CDH2 TES-Enhancer” (CDH2 TES to CDH2 upstream enhancer), and “CDH2 TAD boundary” (CDH2 TAD 5′boundary to 3′boundary). Interaction frequencies were normalized to loading control and Student’s t tests were used for statistical analyses. *p<0.05, **p<0.01, ***p<0.001, and ****p<0.0001. f Top bar plot depicting Hi-C observed/expected values (y-axis) between interacting loci (x-axis) in CDH1 TAD, in PEO1 (black) and HEYA8 (grey). The interacting loci at the CDH1 TAD are as follows: “CDH1-CDH3” (CDH1 TSS to CDH3 TSS), “CDH3-ZFP90” (CDH3 TSS to ZFP90 TSS), “CDH1- ZFP90” (CDH1 TSS to ZFP90 TSS), and “CDH1 TAD boundary” (CDH1 TAD 5′boundary to 3′boundary). Bottom bar plot depicting Hi-C observed/expected values (y-axis) between interacting loci (x-axis) in CDH2 TAD, in PEO1 (black) and HEYA8 (grey). The interacting loci at the CDH2 TAD are as follows: “CDH2 TSS-intron” (CDH2 TSS to CDH2 intronic enhancer), “CDH2 TES-Enhancer” (CDH2 TES to CDH2 upstream enhancer), and “CDH2 TAD boundary” (CDH2 TAD 5′boundary to 3′boundary). Student’s t tests were used for statistical analyses, *p<0.05. g Illustration of 3D genome structure and epigenetic landscape changes in the epithelial and mesenchymal TADs during different EMT states along the EMT spectrum. H3K27ac and H3K27me3 are represented by green and grey respectively. The active compartment A and inactive compartment B are represented by red and blue respectively