Fig. 2: Cell-type-specific CTCF looping regulates PCa-associated genes.
From: MYC reshapes CTCF-mediated chromatin architecture in prostate cancer
a Scatter plots showing the association of CTCF loop strength between two replicates in VCaP and 22Rv1, respectively. n = 167054 and 218739 from left to right, respectively. P-values were calculated using Pearson correlation. b Scatter plots showing the association of CTCF loop strength between VCaP replicate #1 and 22Rv1 replicate #1. n = 217761. P-value was calculated using Pearson correlation. c Scatter plots showing the association of CTCF loop strength between VCaP replicate #2 and 22Rv1 replicate #2. n = 210816. P-value was calculated using Pearson correlation. d Boxplots showing the strength and distances of CTCF loops classified based on cell-type specificity and H3K27ac status of two anchors from the same loop. Box plots indicating the mean (middle line), 25th and 75th percentile (box) and 10th and 90th percentile (whiskers), and n = 24661, 24708, 8804, 17267, 21223, 8967, 12496, 11277, 3348 for boxes from left to right, respectively. P-values were calculated by Wilcoxon signed-rank test. e The number of genes within CTCF loops. The gene numbers were normalized by CTCF loop distances. Box plots indicating the mean (middle line), 25th and 75th percentile (box) and 10th and 90th percentile (whiskers), and n = 24661, 24708, 8804, 17267, 21223, 8967, 12496, 11277, 3348 for boxes from left to right, respectively. P-values were calculated by Wilcoxon signed-rank test. f Average log2 expression fold changes (22Rv1 vs. VCaP) of genes within CTCF loops. Box plots indicating the mean (middle line), 25th and 75th percentile (box), and 10th and 90th percentile (whiskers), and n = 24661, 24708, 8804, 17267, 21223, 8967, 12496, 11277, 3348 for boxes from left to right, respectively. P-values were calculated by Wilcoxon signed-rank test. g KEGG pathway enrichment analysis of genes annotated to the anchors of CTCF loops. The proximity of genes to anchors is restricted to 3Kb. h Upper: A cell-type-specific CTCF binding insulates the interaction between a distal enhancer and TMC5 promoter by forming CTCF-CTCF loops. The 22Rv1-specific CTCF binding was highlighted within a red dashed rectangle. Bottom: TMC5 expression levels in VCaP and 22Rv1 cells based on RNA-Seq data. i Pearson correlation coefficients between DNA methylation ratio of CpGs and CTCF binding affinity at this CTCF site in 20 ENCODE cell lines. Each circle denotes a CpG within this CTCF site. j Scatter plot showing a positive correlation between average DNA methylation levels at this CTCF site and TMC5 expression levels in Changhai 2020 data set. The error band indicates SEM. P-value was calculated using Pearson correlation.
