Fig. 3: Distributions of structural variants across 3D genome architectures.

a Permutation testing was employed to assess the spatial distribution patterns of both pan-cellular and ccRCC specific structural variants across 3D chromatin organizations. The Expected distribution was derived from 1000 iterations of random shuffling of chromosomal regions. b Density of SVs (insertions, deletions, and duplications) across A/B compartments and TADs. SV density, calculated as the number of SVs normalized by the length of corresponding chromosomal regions, is represented as follows: gray bars indicate the background SV density across entire chromosomes; yellow bars show SV density in A compartments; light blue bars represent SV density in B compartments; orange bars depict SV density at TAD boundaries; and dark blue bars illustrate SV density within TAD domains. Enrichment analyses were conducted with proportionality test using R’s proportion test, comparing the proportion of SVs in each region of interest to the proportion of that region’s length in the whole genome. Significance levels are denoted as follows: ****p ≤ 0.0001, ***p ≤ 0.001, **p ≤ 0.01, *p ≤ 0.05. c Density of ccRCC-specific SVs (insertions, deletions, and duplications) across A/B compartments and TADs. ccRCC-specific SVs are defined as those occurring in 786-O or OS-RC-2 but absent in HEK293T. SV density was calculated using the same method as in the legend of (B). Enrichment analyses for these ccRCC-specific SVs were also performed using R’s proportion test, following the same approach as described in (B). d Proportions of ccRCC specific SV subtypes across distinct A/B compartment switching regions in 786-O cell. e Schematic of SV classification based on the positional relationship between ccRCC specific SV breakpoints and TAD boundaries. f Number and proportion of ccRCC specific SV types in 786-O according to (E). g Number and proportion of ccRCC specific SV types in 786-O according to (E).