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. 2023 Jun 22;80(7):187. doi: 10.1007/s00018-023-04830-8

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — GAS, ISRE and composite genes are commonly involved in IFNα- and IFNγ-mediated transcriptional responses and chromatin interactions. A Huh7.5 cells were treated with IFNα (1000 U/ml) or IFNγ (10 ng/ml) for the indicated times. The expression levels of STAT1, STAT2, IRF9 and IRF1 were evaluated by immunoblotting; p phosphorylated, t total. B Expression profile of pre-selected ISGs quantified using qPCR. Cells were left untreated or stimulated with IFNα (1000 U/ml) or IFNγ (10 ng/ml) for the indicated time. Relative expression (over GAPDH) was estimated. n = 3; mean ± SEM. C Venn diagram based on RNA-seq results showing total numbers of uniquely and commonly up-regulated genes in Huh7.5 cells after IFNα or IFNγ stimulation (log2FC > 0.5; p_adj < 0.05). D Number of up-regulated genes (log2 FC > 0.5 and p_adj < 0.05) in each time-point is indicated using color bars (corresponding values—left y-axis). The area of the bar covered with lines represents the number of overlapping genes between analogous time-points for both IFNs. Average gene expression is shown using red lines with symbols (corresponding values—right y-axis). E Heatmaps generated from the expression values of all up-regulated genes in Huh7.5 cell treated with IFNα or IFNγ. Each row represents one gene. Counts were normalized using Z-score. Pre-selected genes are marked on each graph. The color of the gene name corresponds to the binding site recognized in the promoter of the gene. F Gene Ontology terms enrichment analysis of up-regulated genes by IFNα or IFNγ (significant enrichment considered with FDR < 0.05). G Characterization of ChIP-seq peak score and distribution for pSTAT1, pSTAT2, IRF9 and IRF1 in IFNα- and IFNγ-stimulated Huh7.5 cells. Black bars represent a number of peaks called using spp and thresholded using Irreproducible Discovery Rate (IDR) for each time-point separately (corresponding values—left y axis). Red circles, triangles and rhombi represent the maximum, median and mean peak values, respectively (corresponding values—right y axis)