Fig. 2: Epigenetic analyses reveal a ccRCC-activated EPAS1-enhancer.

a Sequencing tracks from ATAC- and H3K27ac ChIP-seq experiments performed in cells from patient #1 at the EPAS1 locus. Activity-by-contact (ABC) analysis was used to predict enhancer-promoter interactions. Additionally, tracks from published data from Capture-C experiments in 786-0 cells³⁴, gained enhancer activity in ccRCC (ccRCC-enhancer)³², ccRCC cancer-cell specific differentially accessible regions (ccRCC-specific DACR) as determined by snATAC-seq³⁵, KIRC hypomethylated CpGs (Beta-value cutoff 0.25, adjusted p-value cutoff 0.01)³⁶ and KIRC-specific ATAC-seq elements are shown³⁷. b Differentially active enhancer regions on chromosome 2 in ccRCC tumors from Yao et al³². Average log₂ fold chance (H3K27ac signal, ten tumors vs corresponding normal tissue) and -log₁₀ adjusted p-value are shown. Significantly regulated elements (adjusted p < 0.05, light blue) that overlap KIRC-specific ATAC sites are depicted in dark blue. Sites highlighted in red overlap KIRC-specific sites, show a positive log₂ fold change and are localized within 5 Mb of the EPAS1 gene. Enhancer enh-1031503 covers elements KIRC_10767-KIRC_10770. For comparison, the H3K27ac signal at the EPAS1 promoter is marked, but not significantly regulated. c ATAC-seq tracks for the different TCGA tumor entities at the ccRCC-enhancer site with gained activity in ccRCC³⁷. KIRC specific ATAC-seq sites 10767-70 are indicated above the tracks. d Spearman’s rank correlation analysis of HIF-2α mRNA expression (TPM: transcripts per million) and accessibility at KIRC_10770 in the KIRC data set. Values are from samples for which both analyses were available (n = 16 different tumors). Gray region depicts 95% confidence interval. Significance was assessed with a two-sided t-approximation test.