Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome

The tissue-specific correspondence of PPI and genomic proximity. (A) The proportion of intra-chromosomal (left) and inter-chromosomal (right) gene pairs with HCT116-related PPI at different C_TG distances. The proportion refers to number of gene pairs with PPIs at fixed C_TG distance/number of all gene pairs at fixed C_TG distance. The background refers to number of gene pairs with PPIs/number of all gene pairs at all C_TG distance. The enrichment degree refers to the proportion/background. The control is one. (B) The proportion of intra-chromosomal (left) and inter-chromosomal (right) gene pairs with HEK293T-related PPI at different C_TG distances. (C) The C_TG distance of gene pairs in fixed 1D genomic distance. The C_TG distance between gene pairs with corresponding PPIs (blue scatters) is more proximal than the median C_TG distance of all gene pairs at all 1D genomic sequence distance (orange line). (D) C_TG distance of gene pairs with MCF-7-specific and MCF-10A-specific PPIs in MCF-7 cell. (E) TP53-, GATA3-, and SMARCB1-related MCF-7-specific PPIs. The distance to TP53 indicates the C_TG distance; the green circle indicates the background distance, the pink scatter indicates MCF-7 fitness genes, and the dashes indicate genomic proximal neighbors.