Figure 10. In the absence of TGF-βR signaling, SMAD4 largely binds to DNA and mediates epigenetic control of TGF-β target genes in naive CD8⁺ T cells.

(A) Venn diagram showing the number of SMAD4 common peaks between WT (pool of 3 mice) and R2KO (pool of 5 mice) naive CD8αβ⁺ T cells. (B) The proportions of SMAD4 peaks associated with promoter, 5′ UTR, 3′ UTR, exon, intron, and intergenic regions in WT and R2KO naive F5 CD8αβ⁺ T cells. (C) Enriched heatmaps showing the SMAD4 occupancy signals in genomically aggregated TSS regions in WT and R2KO CD8⁺ T cells. Each panel represents 2 kb upstream and downstream of the TSSs. (D) Venn diagram showing the overlap between SMAD4 ChIP-seq peaks and RNA-seq DEGs. (E) SMAD4-binding ChIP-seq peaks in WT (blue), R2KO (green), or SKO control (orange), in corresponding genes. (F) Transcription factor (TF) top motifs in SMAD4-binding sites in WT and R2KO CD8⁺ T cells. The x axis represents the log(P value) of the motif enrichment, and the y axis represents the fold change of the motif enrichment. (G) The 3 top motifs found by hypergeometric optimization of motif enrichment (HOMER) analysis among SMAD4-binding peaks in WT and R2KO CD8⁺ T cells. (H) qPCR-based ChIP analysis of SMAD4 on the promoters/enhancers of Smad7, Skil, and Itgae in WT, R2KO, and SKO F5 naive CD8αβ⁺ T cells. Each data point represents a pool of 3–5 mice. (I) qPCR-based ChIP analysis of H3K27ac on the promoters/enhancers of Smad7, Skil, and Itgae in WT, R2KO, SKO, and R2SKO F5 naive CD8αβ⁺ T cells. Each data point represents a pool of 3–5 mice.