Supplementary Figure 10: Contribution of H3K27ac ChIP and chromosome conformation to HiChIP EIS.

(a) Left, proportion of H3K27ac ChIP peaks within EIS differential loop anchors that are cell type specific (log₂ (fold change) > 1) or shared across all three subtypes. Right, global correlation of EIS and H3K27ac ChIP fold change in different T cell subset pairwise comparisons. (b) Same as a, but using HiChIP 1D differential signal at EIS biased loop anchors. (c) Overlap of H3K27ac HiChIP and bins of Hi-C loops with increasing T cell subset and GM H3K27ac ChIP–seq signal. (d) Overlap of CD4⁺ capture Hi-C¹⁴ with total and differential T cell subset HiChIP loops. Naïve 4X and 16X corresponds to EIS fold-enrichment over T_H17 and T_reg, T_H17 and T_reg 4X and 16X corresponds to EIS fold-enrichment over Naïve. (e) T_reg-specific loops at the LRRC32 promoter not observed in other H3K27ac HiChIP T cell subsets nor in CD4⁺ capture Hi-C data¹⁴.