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Fig. 3 | Genome Biology

Fig. 3

From: Promoter-like epigenetic signatures in exons displaying cell type-specific splicing

Fig. 3

Enrichment of chromatin epigenetic marks on regulated exons. a Differential signals (log2, Y-axis) for ‘more included’ (blue) or ‘less included’ (red) exons from the seven cell pairs used, are represented for 11 ChIPSeq datasets corresponding to different epigenetic marks, CTCF, and input DNA (control). The boxplots correspond to the distribution of the average differential signal over the length of each regulated exon. Wilcoxon rank-sum tests with Bonferroni correction were calculated for the two distributions, significance levels are indicated: * (0.05 > P > 0.01), ** (0.01 > P > 0.001), *** (0.001 > P). CTCF, H3K9ac, H3K4me3, and H3K27ac have significantly higher signal in ‘more included’ than in ‘less included’ exons, while input DNA control shows the opposite trend. b Validation of H3K9ac enrichment over H3 by ChIP. Average and standard deviation of log2 of the fold change in H3K9ac signal over total H3 signal in regulated (alternative) and constitutive exons from four different genes. Values are from three independent replicates. White bars in the lower panel represent inclusion level ratios between the two cell lines for the regulated exons, as determined by RNASeq. A general association between exon inclusion and higher levels of H3K9 acetylation is observed. cf Differential ChIPSeq signals (average and standard error of the mean) for CTCF, H3K9ac, H3K27ac, and H3K4me3 are represented for ‘more included’ exons (blue) and ‘less included’ exons (red) in a 800 bp-window around the middle of the regulated exon (AS) and flanking not regulated (notAS) upstream (left) and downstream (right) exons. Significance levels are indicated by * (0.05 > P > 0.01), ** (0.01 > P > 0.001), *** (0.001 > P), and ns (P > 0.05). Differential accumulation of marks is generally specific of regulated exons

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