Supplementary Figure 6: Global enhancer connectome characterization in T cell differentiation.

(a) ChromHMM classification of union T cell loop anchors. (b) Contact distance distribution of union T cell loops. (c) Left, agreement in signal observed per loop between samples. The quantile–quantile plot shows modest enrichment above random pairings. Right, PCA on residual signal clusters samples first by naive versus memory cell types (PC1) and then by donor identity (PC2, PC3). (d) Overlap of differential interactions between naive, T_H17, and T_reg subtypes. Biased interactions were obtained by performing pairwise comparisons between T cell types and analyzing the top 5% enriched and top 5% depleted EIS in each T cell subtype. (e) ChromHMM annotation of total loops, differential loops, and shared loops in all three T cell subtypes. O corresponds to other loop anchors not classified as enhancer or promoter. (f) Number of connections for different classes of loop elements. (g) Quantification of promoters skipped before an enhancer reaches its loop target.