Fig. 3

Intragenic enhancers and differential transcript expression. Relative enrichment z-scores of RNAPII on the most upstream TSS (TSS1) (a) and the second TSS (TSS2) (b) when there is an active (left red violin plots) or silent (right blue violin plots) enhancer between both TSSs and it sits at a minimum distance of 1000 nt from either one. The yellow violin plots in the middle represent the z-score distribution of all TSS1-TSS2 pairs, with or without predicted enhancers and the dashed green line represents the median value of this distribution. c A TSS1-TSS2 event in gene MAGED1 with a silent enhancer in K562 close to TSS2 (light green box). The black boxes indicate the intragenic 1500 nt windows analyzed to search for enhancers. Dark green boxes indicate the significant windows and light green indicates the candidate silent enhancer. RNA-Seq data from K562 and GM12878 cell lines (2 replicates each) is shown below, together with the H3K27ac and DNase I hypersensitive sites tracks from ENCODE. The long intron separating the two TSSs is cut in the middle for simplicity