(A) Pipeline for ChIA-PET data processing and identification of chromatin interactions. (B) Enhancers per gene and genes per enhancer for each cell line. For enhancers per gene, all expressed genes (fragments per kb per million mapped reads [FPKM] >1) were included; for genes per enhancer, all enhancers located in RNA Pol II peak anchor regions were included. Box plot represents the median and the 25% and 75% quantiles, with lines at 1.5 times the IQR. The significance for each pair comparison was tested using the Kolmogorov-Smirnov test (^†P < 2.2 × 10^–16).The analysis was normalized by adjusting for sequencing depth. (C) Correlation between RNA expression and chromatin interaction across the 4 cell lines. The expression level was measured by FPKM transformed by log₂, and chromatin interactions were measured by the number of promoter PETs. The correlation efficient was calculated by Spearman’s correlation, and P values are shown. (D) Significant gain and loss of RNA Pol II–associated chromatin interactions in the 4 cell lines. The 3 solid lines show the distributions of the 3 PCa cell lines compared with benign cells (RWPE-1), whereas the 3 broken lines show the distributions among the 3 PCa cell lines. The significant gain or loss interactions were obtained using the DNB model. The total number of interactions that were significantly altered between cell lines are listed accordingly. (E) Scatter plot shows the correlation between changes in gene expression and changes in promoter-associated chromatin interactions. Graphs show Spearman’s correlation coefficients for the top 10%, 20%, 40%, 60%, and 80% differentially expressed genes (right panel). FC, fold change. (F) Total number of PETs at promoter regions in the 4 cell lines. Genes are ranked by increasing number of PETs. Eight representative genes are labeled 1 through 8 in the plots.