Fig. 2: 3D genome architectural reorganization correlates with gene expression alterations in ccRCC.
From: Structural variation drives enhancer hijacking via 3D genome disruption in ccRCC
a Stacked bar chart showing frequencies of whole-chromosome A/B compartment shifts in 786-O and OS-RC-2 compared to HEK293T. b Box plot showing gene expression distribution: the box spans the interquartile range (IQR), the center line marks the median, and the whiskers extend to 1.5×IQR (or to the maximum/minimum values if within range). Gene expression comparisons are presented as Log2FC (786-O vs HEK293T), with p-values calculated using the Wilcoxon rank-sum test. c Volcano plot highlighting differentially expressed genes (orange: significantly upregulated; green: significantly downregulated) and cancer-related genes in regions with B-to-A compartment shifts. Differentially expressed genes are defined by |Log2FoldChange | > 1 and adjusted p value < 0.05, with examples of cancer-related genes circled in black. d Pearson correlation heatmap of chr15 in OS-RC-2 and HEK293T. e IGV images display an example of A/B compartment shifts on chromosome 12 in 786-O and OS-RC-2 versus HEK293T. Assignment of A (red) and B (blue) compartments is based on eigenvector values > 0 and < 0. Gene density in the genome is shown as histograms, and enhancer activity is marked by H3K27ac ChIP-seq peaks, presented as histograms in 786-O (yellow track) and OS-RC-2 (blue track). The red box indicates a common B-to-A event covering the BTG1 gene in both cancer cell lines. f Venn plot depicting the overlap of TADs derived from 10-kb resolution interaction matrices across the three cell types, with the number of TADs in each category shown. g, h Examples of TAD alterations in regions of interest (G: chr7:31,740,000-33,130,000, H: chr5:156,410,000-157,740,000) in OS-RC-2 compared with HEK293T. Boxes in the interaction heatmaps delineate TADs, with involved genes displayed (RefSeqGene). i Box plot showing the distribution of TAD length: the box spans the interquartile range (IQR), the center line marks the median, and the whiskers extend to 1.5×IQR (or to the maximum/minimum values if within range). P values were calculated using the Wilcoxon rank-sum test. j Box plot showing gene expression distribution: the box spans the interquartile range (IQR), the center line marks the median, and the whiskers extend to 1.5×IQR (or to the maximum/minimum values if within range). Gene expression comparisons are presented as Log2FoldChange (ccRCC-common TAD region vs conserved TAD region), with P values calculated using the Wilcoxon rank-sum test. k Jensen- diseases pathway enrichment of differentially expressed genes located in ccRCC-common TADs. P values were obtained by Fisher’s exact test using EnrichR.
