Fig. 6: TRIM28 and CTCF exhibit co-localization in activated CD8⁺ T cell genome.

a Distribution of TRIM28 binding peaks in activated WT CD8⁺ T cells. b Proportions of loops^Activated occupied by TRIM28 in activated CD8⁺ T cell. c Proportions of loops disappeared after Trim28 deficiency in the loops^Activated bound by TRIM28. d Gene ontology enrichment analysis for the 530 genes located in the anchor regions of the loops in (c). e Proportions of upregulated genes during CD8⁺ T cell activation in the 530 genes located in the anchor regions of the loops in (c). f Aggregate plot of H3K27ac, H3K27me3 and H3K9me3 modification at ± 5.0 Kb in CD8⁺ T cells of the TRIM28 binding sites in activated WT CD8⁺ T cells. g Genome browser views showing TRIM28 binding sites and histone modifications around Ifng, Tbx21 and Id2 in activated WT CD8⁺ T cells determined using ChIP-seq data. h Motif enrichment analysis in the TRIM28 binding sites. i Co-immunoprecipitation (IP) of CTCF by an anti-TRIM28 antibody in the activated WT CD8⁺ T cells. j Venn diagram showing the overlap between CTCF peaks (blue) and TRIM28 peaks (red) in activated WT CD8⁺ T cells. k Proportions of WT_Na. vs. WT_Act specific genes occupied by TRIM28 in activated state (left). Proportions of WT_Na. vs. WT_Act specific genes both occupied by TRIM28 and CTCF in activated state (right). l Genome browser view of TRIM28, CTCF, RNA PII binging signals and 3D genome interactions around the Il2 gene in activated WT CD8⁺ T cells. m Heatmap displaying TRIM28, CTCF, H3K27ac and RNA PII at TRIM28 binding sites in activated WT CD8⁺ T cells using ChIP-seq and CUT&Tag data. The upper panel showed the TRIM28 binding sites with CTCF in activated WT CD8⁺ T cells. The lower panel showed the TRIM28 binding sites without CTCF in activated WT CD8⁺ T cells. Statistical significance was tested by Chi-squared test (b), unpaired two-tailed Student’s t test (c) and hypergeometric test (j). Data are representative of two (i) independent experiments.