Fig. 5
From: RAD21 is the core subunit of the cohesin complex involved in directing genome organization
RAD21 up-regulation is involved in breast cancer accompanied with chromatin architecture alternatives. A The survival plot based on the expression of RAD21 (orange line denotes the high expression group; blue line denotes the low expression group). B Gene expression of RAD21 in breast cancer and normal samples from TCGA database. C Example super-resolution images of MCF10A, MDA-MB-157, SK-BR-3 and HCC1395 cells. Scale bar, 5 μm. Deconvolution was applied to improve the imaging resolution and signal to noise ratio. D Extent of RAD21 clustering in cells from (C) were quantified by heterogenetic level (n > 30 per condition). The lower quartile, median and upper quartile values were labelled in the box. E Heatmap showing differentially expressed genes (p < 0.05, Benjamini-Hochberg; log2 Fold change > 1 or log2 Fold change < -1) in RAD21-OE cells vs. control cells, RNA-seq analysis was done in HeLa cell line. Some marker genes associated with breast cancer were shown in the right of heatmap. F Above: Boxplots showing gene expression changes in regions with compartment switching compared to the stable. P-values: Wilcoxon rank-sum test. Bottom: An example of expression level changes of cancer related genes (CEMIP) in the regions from B to A compartments upon RAD21 over-expression. G Quantification of the difference of TAD score (TAD score = intra-TAD / inter-TAD) between RAD21-OE and control. TADs are stratified into those that contain up-regulated genes or down-regulated genes, or TADs containing genes that show no significant difference in expression. Wilcoxon rank-sum test shows a significant decrease in TAD score between TADs that contain an up-regulated or down-regulated genes and TADs that do not contain a significantly affected genes