Figure 5. IL-2- and αKG-sensitive CTCF association correlates with changes in genomic organization.

(A–D) In situ Hi-C or CTCF ChIP-seq experiments were performed with primary CD4⁺ T cells polarized in Th1 conditions and maintained in high IL-2, low IL-2, or low IL-2 with αKG for two days. (A,B) UCSC genome browser tracks displaying a Hi-C (A) PC1 analysis to define transcriptionally permissive (PC1 positive; black) versus inert/or transcriptionally repressive (PC1 negative; grey) genomic compartments, (B) an analysis of outer TAD boundaries and (A,B) ChIP-seq CTCF tracks as described in 4C. (C, D) Circos plots for genomic regions surrounding Hlx (Chr1:184,000,000–187,200,000) and Cxcr4 (Chr1:128,800,000–131,040,000) indicating the probability for genomic interactions from the in situ Hi-C analysis. The minimum probability of interaction shown is a p value of ≤0.0001 with the increased weight of a line indicating a higher significance for the interaction (lower p value). (E) UCSC genome browser tracks displaying CTCF ChIP-seq from Th1 cells exposed to high IL-2, low IL-2, or low IL-2 with αKG, and an ATAC-seq analysis of NP-specific CD8⁺ T cells isolated 9 days after influenza infection that were sorted into CD25^hi or CD25^lo populations. Regions displayed were associated with the interaction loops identified in the circos plots in (C, D). Blue arrows indicate IL-2- and αKG-sensitive CTCF sites and yellow arrows indicate ATAC-seq changes. See also Fig. S4–6.