Fig. 3

Non-coding RNAs are frequently near or overlapping SEs. a Ternary plot of lncRNA expression in Th1, Th2, and Th17 cells. Color scale indicates concentration of lncRNAs. Notable examples of lncRNAs that are lineage specific and located near SEs are shown. RNA-seq data are from [26]. b Ternary plot of miRNA expression in Th1, Th2, and Th17 cells. Color scale indicates concentration of miRNAs. MiR-155 and miR-142 are labeled as examples of miRNAs located near SEs. Small RNA-seq data are from [29]. c LncRNAs expressed from SEs are cell-type specific. (Upper panel) NeST, a lncRNA (or eRNA) that is expressed from the SE at the Ifng locus. NeST, Ifng, and the SE are active in Th1 cells, but not in Th2 or Th17 cells. (Bottom pane) miR-155 is expressed in Th17 cells and is located near multiple SEs that are active in T helper cells. d A SE is more likely than a CE to be associated with a lncRNA. Proportion of SEs or CEs that are located within 100 kb of a lncRNA expressed in Th1, Th2, or Th17 cells (left). Proportion of lncRNAs (or eRNAs) that are directly transcribed from SEs or CEs, in Th1, Th2, and Th17 cells (right) (p-value < 2.2e-16 for all three comparisons)