Fig. 3

PCHi-C interactions and enhancer activity predict change in gene expression. a Change in gene expression at protein coding genes (log₂ fold change, y-axis) correlates with the number of PIRs gained or lost upon activation (x-axis). b Fold change at transcribed sequence within the intergenic subset of regulatory regions (‘eRNAs’) was more likely to agree with the direction of protein-coding gene fold change when the two are linked by PCHi-C (red) in activated CD4⁺ T cells compared to pairs of eRNA and protein-coding genes formed without regard to PCHi-C derived interactions (background, grey, p < 10⁻⁴). Interactions were categorised as control (present only in megakaryocytes and erythroblasts, our control cells), invariant (‘invar’; present in non-activated and activated CD4⁺ T cells), ‘loss’ (present in non-activated but not activated CD4⁺ T cells and significantly downregulated at FDR < 0.01) or ‘gain’ (present in activated but not non-activated CD4⁺ T cells and significantly upregulated at FDR < 0.01). c Gain or loss of PIRs upon activation predicts change in gene expression, with the estimated effect more pronounced if accompanied by upregulation or downregulation at an eRNA. Points show estimated effect on gene expression of each interaction and lines the 95% confidence interval. PIRs categorised as in (b). eRNAs categorised as no (undetected), invariant (‘invar’, detected in non-activated and activated CD4⁺ T cells, differential expression FDR ≥ 0.01), up (upregulated; FDR < 0.01) or down (downregulated; FDR < 0.01). Bar plot (top) shows the number of interactions underlying each estimate. Note that eRNA = down, PIR = gain (light gray) has only one observation so no confidence interval can be formed and is shown for completeness only