Figure 6.
Mechanistic insight into hypoxia inducible changes in chromatin accessibility.
(A–D) Overlap of differential open chromatin regions (DORs) identified by ATAC-seq (n = 2) with HIF subunit binding sites identified by ChIP-seq (n = 2) in HeLa cells. (A) Overlap of 24 h 1% oxygen (hypoxia (Hpx)) or 24 h, 100 µM VH298 DORs with of HIF subunit binding sites. Percentage of DORs containing a HIF binding site (HIF-1α, HIF-2α or HIF-1β) are displayed. (B) Overlap of 24 h hypoxia or VH298 up-regulated DORs with of HIF subunit binding sites. Percentage of promoter, gene body and intergenic DORs containing a HIF binding sites (HIF-1α, HIF-2α or HIF-1β) are displayed. (C) Overlap of both VH298 and 24 h hypoxia up-regulated DORs, 24 h hypoxia specific up-regulated DORs or VH298 specific up-regulated DORs with HIF subunit binding sites. Percentage of DORs containing a HIF binding site (HIF-1α, HIF2α or HIF1β) are displayed. (D) Overlap of HIF-1beta dependent/independent and reoxygenation sensitive/insensitive 24 h hypoxia up-regulated DORs with HIF subunit binding sites. Percentage of DORs containing a HIF binding site (HIF-1α, HIF-1β or HIF-2α) are displayed. (A–D) Statistical significance was determined via hypergeometric test, ** P < 0.01, *** P < 0.001. (E) Metagene plot of control condition (0 h hypoxia) ATAC-seq signal (RPKM) at the indicated regions. (F) Box plot of H3K4me3 ChIP-seq (n = 2) signal (RPKM) in HeLa cells exposed to 0 h (control) and 6 h hypoxia at 24 h hypoxia up-regulated DORs (centre ±1 kb). Statistical significance was determined via Wilcoxon signed-rank test, *** P < 0.001. (G) ATAC-qPCR analysis in HeLa cells cultured at 21% oxygen, transfected with control or KDM5A siRNA, and exposed to 0 h (control) or 24 h hypoxia. Graphs show mean (n = 3) ± SEM, statistical significance was determined via one-way ANOVA with post-hoc Tukey test, * P < 0.05, ** P < 0.01, *** P < 0.001.