Fig. 2: Genomic and epigenomic characteristics of IFNa-induced genes and Epromoters.

a Top10 Gene Ontology enrichment for the biological process of genes associated with “induced gene only” (blue) and “induced Epromoter & gene expression” (green). No enrichment was found in the “induced Epromoter only” category. Data plotted are the adjusted P-value (−log₁₀ scale) of the enrichment. b Percentage of conserved ISGs²¹ found in the “induced gene only” and “induced gene & Epromoter” sets. Chi-square test was performed and P-values are annotated. c Average profiles of ChIP-seq signals for the TFs STAT1, STAT2, IRF9, and IRF1 in K562 cells stimulated with IFNa for 6 h. The groups shown were defined in Fig. 1e. The solid line represents the mean of the signal while the colored area represents the 95% confidence interval. The left panels display the average profiles set at the maximum scale, while the right panels display the same profiles set at a lower scale. d Average profiles of ChIP-seq signals for the histone modifications, H3K27ac, H3K4me3 and H3K4me1 in K562 cells non-stimulated (blue) or stimulated with IFNa for 6 h (red). The solid line represents the mean of the signal. e Top de novo motifs found enriched in “induced gene only”, “induced gene & Epromoter” and “induced Epromoter only” sets, using the HOMER tool⁷³. The enrichment adjusted P-value is shown. f Motif enrichment analysis in promoter regions from the groups defined in Fig. 1E using the HOMER tool. Only the top 10 motifs for each promoter set are shown. The data shown is the adjusted P-value (−log₁₀). g Comparison of the relative number of binding sites per promoter between the “induced Epromoter and induced gene” versus the “induced genes only” sets. The data shown is the adjusted P-value (−log₁₀) of the comparison. h Pie-charts showing the percentage of promoters from the indicated datasets that contain either none (gray), one (blue) or two or more ISRE-binding sites (red) (merged sites for IRF1–9 and STA1-2 motifs) based on the Jaspar 2020 annotation⁷⁴ by default (All ISRE sites) or with a P-value < 1e-4 (High confidence).