Fig. 4

Effect of intragenic enhancers on splicing. a From the 2205 genes found to have active enhancers, 77 of them have regulated events. From the 1527 genes with active and silent enhancers, 148 have regulated events, and from 2381 genes with silent enhancers, 100 have regulated events. b Enriched Gene Ontology processes in the genes with active or silent enhancers and with regulated events, compared to genes with intragenic enhancers but no regulated events (Additional file 1: Table S3). c Example of a regulated alternative splicing event in the gene MACF1. The cassette exon shows increased inclusion in K562 with delta-PSI = 0.72 (PSI = 0.86 in K562 and PSI = 0.14 in GM12878). Two active enhancers are predicted in K562 in the area of the regulated exon (light red boxes). Intragenic scanned windows are indicated as black boxes, and significant windows are dark red boxes. One of the predicted enhancer regions shows binding of PU.1 in K562 (2 replicates) but no biding in GM12878 (2 replicates). 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