Fig. 4: Compartment switching dysregulates cancer-related genes.

A Volcano plot showing the DEGs (fold change >2, p value <0.05) between Arid1a WT (Ad-GFP) and KO (Ad-Cre) AB17 cells. The green and red dots represent down- and up-regulated genes post Arid1a deficiency, respectively. B The enrichment analysis on down- (Left) and up-regulated (Right) genes. The top ten significantly enriched terms were shown (p value <0.01). The color-coded circles symbolize the enriched GO terms and pathways. C Fold change (Ad-Cre/Ad-GFP log2) of mRNA expression (FPKM) of the genes residing at regions with compartment switching. D Venn diagrams displaying the overlap of DEGs and A/B compartment switch-related genes (Left). The heatmap showing the expression profiles of the switching compartments controlled-genes with triplicate datasets, of which down- and up-regulated cancer-related genes labelled by green and red pentagrams, respectively (Right). E qRT-PCR for the compartment switching-controlled genes in Arid1a WT (Ad-GFP) and KO (Ad-Cre) AB17 and Q506 hepatocytes as well as MEFs (193-4 and 102-2 cells) with three biological replicates. Error bars were painted by SEM. p value was calculated by a two-tailed Student’s t-test. mRNA expression of Gapdh was employed as an internal control.