Fig. 2

Super-enhancers in T helper cells. a Ternary plot of P300 density at SEs in Th1, Th2, and Th17 cells (left) or gene expression in the same cells (right). Each dot is a SE or gene. T helper cell SEs are largely shared between all three subsets. Axes indicate relative factor density between Th1, Th2, and Th17 cells. Color scale indicates concentration of SEs (note: area of graph occupied by color scale for gene expression is much smaller than area of color scale for P300 density, and is not visible because it is covered by overlapping points). ChIP-seq data are from [24, 25]. RNA-seq data are from [26]. b Ternary plot of P300 density at SEs in mESC, stimulated B cells, and Th17 cells. Color scale indicates concentration of SEs. Some SEs are shared between B cells and Th17 cells, but are distinct from mESCs, a distantly related cell lineage. B cell ChIP-seq data are from [74]. c (Top) Il17a and Il17f are regulated by a Th17-specific SE spanning both genes. Also, a non-coding RNA is transcribed 3' of Il17f. (Bottom) Cd28, Ctla4 and Icos are regulated by two SEs active in Th1, Th2, and Th17 cells. Similar levels of expression and P300 density are seen in all three cell types. d Genes from both the Th17 SE module and the Th17 gene expression module which have lower expression when treated with the RORγt inhibiting drugs, TMP778 or TMP920. They are also expressed lower in RORγt-deficient Th17 cells. CE-genes from Th17 cells are generally unaffected (SE examples were chosen because of known disease relevance, CE examples shown were chosen arbitrarily). Data are from [27]