Fig. 4

p63- and CTCF-bound Ctr-OCRs are involved in chromatin loops regulating epidermal genes. a Highly expressed genes are associated with more DNA loops. Genes were divided in quarters according to their expression levels in keratinocytes. The number of connected DNA loops associated with each group of genes were plotted in the bottom bar chart. b DE genes were associated with more connected DNA loops when compared to all expressed genes. ***, p < 0.001, Wilcoxon signed-rank test. c DE genes were associated with more connected DNA loops with p63-bound Ctr-OCRs when compared to all expressed genes. d DE genes were associated with more connected DNA loops with CTCF-bound Ctr-OCRs when compared to all expressed genes. e Overlapping of genes mapped by CTCF-bound Ctr-OCRs (orange) and p63-bound Ctr-OCRs (blue). f GO annotation of the 96 genes potentially co-regulated by p63 and CTCF. g p63-bound and CTCF-bound Ctr-OCRs were involved in the same or different loops connecting the promoters of the 96 genes. 60 genes were regulated by the same loops with both p63-bound and CTCF-bound Ctr-OCRs: (1) in 12.6% cases, p63-bound Ctr-OCR located at one anchor while CTCF-bound Ctr-OCR located at the other anchor of the loop; in the majority cases, p63-bound and CTCF-bound Ctr-OCRs were both present at the (2) promoter (70.6%) or (3) enhancer (16.8%) of the DNA loops. h The left 36 genes were co-regulated by connecting DNA loops with p63-bound and CTCF-bound Ctr-OCRs at enhancers of different loops. i PIGV is shown as an example of G (1), which is connected by the DNA loop pair1402, bridging the PIGV promoter (with a CTCF-bound Ctr-OCR) and a distal enhancer (with a p63-bound Ctr-OCR). j KRT5 is shown as an example of G (3), which is connected by the DNA loop pair25496, bridging the KRT5 promoter and a distal enhancer (with both CTCF-bound and p63-bound Ctr-OCRs). The blue arrows pointed to the p63 BSs while the green arrows pointed to the CTCF BSs