Fig. 5: Trim28 ablation alters the chromatin accessibility and spatial structure in activated CD8⁺ T cells.

a Volcano plot comparing chromatin accessibility of naive Trim28^-/- CD8⁺ T cells (Trim28^-/- _Na) VS naive WT CD8⁺ T cells (WT_Na). The X-axis was the Fold change (log₂) of Trim28^-/- versus WT. Every sample has two replicates. b Volcano plot comparing chromatin accessibility of activated Trim28^-/- CD8⁺ T cells (Trim28^-/- _Act) VS activated WT CD8⁺ T cells (WT_Act). The X-axis was the Fold change (log₂) of Trim28^-/- versus WT. Every sample has two replicates. c Mean ATAC-seq coverage at the Il2, Gzmb and Ifng genes. d Chromatin regions specifically accessibility in naive WT CD8⁺ T cells (blue) and activated WT CD8⁺ T cells (red) were analyzed for enrichment in the activated Trim28^-/- CD8⁺ T cells versus activated WT CD8⁺ T cells by peak set enrichment analysis (PSEA). e Venn diagram of TADs of activated WT and activated Trim28^-/- CD8⁺ T cells based on domain scores. TADs, topologically associating domains. Two replicates were analyzed separately to assess consistency, and results were then combined. Details see methods. f Hi-C interaction matrix of the regions in activated WT and activated Trim28^-/- CD8⁺ T cells around the Il2 gene. g Venn diagram of chromatin loops of activated WT and activated Trim28^-/- CD8⁺ T cells (left). Heatmap of loop strength difference (right). Two replicates were analyzed separately to assess consistency, and the results were then combined. For details see methods. h Chromatin specifically loops in naive WT (blue) and activated WT CD8⁺ T cells (red) were analyzed for enrichment in the activated Trim28^-/- CD8⁺ T cells VS activated WT CD8⁺ T cells by loop set enrichment analysis (LSEA). i APA (aggregate peak analysis) plot for the selected Loops^naive and selected Loops^Activated (loop strength > 30) in naive, activated WT and activated Trim28^-/- CD8⁺ T cells. j Genome browser view of chromatin accessibility, gene expression and 3D genome interactions around the Il2 gene in activated WT and activated Trim28^-/- CD8⁺ T cells. k Heatmaps displaying chromatin accessibility of loop anchors of three types of loops in activated WT and activated Trim28^-/- CD8⁺ T cells. Statistical significance was tested by unpaired two-tailed Student’s t test (i) and Chi-squared test (k).