Extended Data Fig. 10: Pro-inflammatory genes are induced by SARS-CoV-2 infection concurrent with increased promoter activity and H3K4me3 levels.

a. A scatter plot showing good correlation between the ABC score (x-axis) and the true transcriptional changes of pro-inflammatory (PIF) genes by SARS-CoV-2 (y-axis, RPB1 ChIP-Seq). But the quantity of true changes (y axis) is much higher than the modelled changes based on ABC scores (x-axis), as all the data points are above the diagonal (also see Fig. 6c for revised ABC-P² scores). Error bands indicate the 95% confidence interval of the regression estimate. b. Bar graphs showing the fold changes of two key PIF genes, IL6 and CXCL8, in several conditions: true RPB1 ChIP-Seq fold changes after SARS-CoV-2 infection (TXN); fold changes modelled by ABC score; modelled by ABC algorithm with inclusion of promoter H3K4me3 strength (ABC-P); modelled by ABC algorithm with inclusion of a square of promoter H3K4me3 strength (ABC-P²). Promoter strength is required to revise the ABC algorithm to better model transcriptional increases of PIF genes caused by SARS-CoV-2 infection. c. Snapshots of Hi-C matrices (bin size: 5 kb) and calibrated ChIP-Seq tracks for indicated factors at another key gene loci coding for pathologically critical PIF cytokines in COVID-19 patients: CXCL8 (encoding cytokine IL-8). Red asterisks show reduced H3K27ac peaks. Black arrows show increased H3K4me3 peaks at its promoter by SARS-CoV-2 infection. The intra-TAD interactions were weakened throughout the TAD. Color scales indicate Hi-C contact frequencies. d. Barplot showing the numbers of total, gained or reduced H3K4me3 ChIP-Seq peaks after SARS-CoV-2 infection for 24hpi (0.1 MOI). e. Hallmark signature analysis of genes close to H3K4me3 peaks gained in virus-infected condition show signatures associated with TNF-alpha, TGF-beta signaling or inflammatory responses, which are associated with pathological symptoms in COVID-19 patients. f. Motif analysis of H3K4me3 peaks increased in SARS-CoV-2 infected cells shows that the top ranked motifs are those of IRF1/2 and Jun/AP1, suggesting the potential roles of these transcription factors in transcriptional activation of inflammation genes. Motif analysis was done by HOMER, and the P values and percentages of sites with motifs are shown. g. Snapshots of Mock and HCoV-OC43 Hi-C contact matrices (bin size: 5 kb) and ChIP-Seq tracks for indicated factors at the CXCL8 (encoding IL-8) loci. This is from the same region as in panel c. In comparison to SARS-CoV-2 effect in panel c, HCoV-OC43 caused no reduction of H3K27ac peaks (Red asterisks), and no obvious H3K4me3 increase at its promoter (black arrows). These asterisks and arrows point to the same peaks as those in panel c. Color scales indicate Hi-C contact frequencies.