Fig. 4: TGFβ priming regulates chromatin accessibility and histone modification to suppress the inflammatory action of TNF and facilitate osteoclastogenesis.

Human CD14(+)-monocytes were treated with or without TGFβ priming for 3 days, followed by TNF stimulation for 0 or 1 day. a Volcano plot of ATAC-seq analysis of TNF-induced differentially accessible peaks at day 1 (gray dots) with significant (FDR < 0.01) and greater than twofold changes between non-priming and TGFβ-priming conditions. Data are from two biological replicates. Blue dots: peaks associated with ISGs. Red dots: peaks associated with osteoclast and TGFβ signaling genes. b Pathway analysis of genes associated with the significantly differentially accessible peaks identified in a. c, d Normalized ATAC-seq tag-density (heatmap in c) and tag counts (boxplots in d) of differentially accessible peaks associated with non-priming or TGFβ-priming genes. e Boxplots showing normalized ATAC-seq tag counts of differentially accessible peaks associated with ISGs or osteoclast genes. f Heatmap of normalized H3K4me3 Cut&Run-seq tag-density of the differentially accessible peaks associated with non-priming or TGFβ-priming genes. g Average tag density profile of normalized H3K4me3 Cut&Run-seq peaks associated with ISGs or osteoclast genes. Blue: Non-priming; Red: TGFβ-priming. h Heatmap of normalized H3K27me3 Cut&Run-seq tag-density of the differentially accessible peaks associated with non-priming or TGFβ-priming genes. i Average tag-density profile of normalized H3K27me3 Cut&Run-seq peaks associated with ISGs or osteoclast genes. Blue: Non-priming; Red: TGFβ-priming. j Heatmap of normalized H3K27ac Cut&Run-seq tag-density of the differentially accessible peaks associated with non-priming or TGFβ-priming genes. k Boxplots showing normalized H3K27ac Cut&Run-seq counts of peaks associated with ISGs or osteoclast genes. l Average tag-density profile of normalized H3K27ac Cut&Run-seq peaks associated with ISGs or osteoclast genes. Blue: Non-priming; Red: TGFβ-priming. m, n Representative IGV tracks displaying normalized tag-density profiles for ATAC-seq, H3K4me3, H3K27me3, and H3K27ac Cut&Run-seq signals at ISG (m) and osteoclast gene loci (n). d, e, k, m, n Data are representative of 2 biological replicates. Data are presented as normalized tag density ±2 kb (c) or 5 kb (f, h, j) around peak centers. d, e, k *p < 0.05; ***p < 0.001, ****p < 0.0001; ns, not statistically significant by two-way ANOVA with Bonferroni’s multiple comparisons test. Boxes represent data within the 25th to 75th percentiles. Whiskers depict the range of min to max. Horizontal lines within boxes represent median values. Source data are provided as a Source Data file.