Figure 4.

Some histone mark signals are higher in internal exons than in introns in a transcription-dependent manner. (A) For highly expressed genes, the average histone mark signal in exon-expression groups (low and high) (see Fig. 1) was compared to the respective medium-expressed exons to determine whether the signal was above (yellow), below (green) or at the same level (gray). The classes were determined by calculating the fold change (log₂) of the average signals in the high-expression and low-expression categories to the average signal in the medium-expression one and then further discretized to above (>0.25), below (<–0.25) or at medium (between –0.25 and 0.25) level. (B) For the alternative hypothesis, that the signal in exons (in each exon-expression group) is higher than in corresponding succeeding introns, paired Wilcoxon signed rank test P-values (-log₁₀) are depicted below each histone mark. Asterisks indicate significant (<0.001, horizontal black line) P-values. Highly relevant histone marks showing (1) any of the major identified trends in A; (2) significantly higher signal in exons than introns (B); and (3) lack of preferential accumulation at TSS-proximal regions (manual inspection) are highlighted (A). (C) Footprints of H3K36me3 (red) and H3K27me3 (blue) signals (±1-kb window) in human T-cells centered on intron/exon junctions of internal exons in highly expressed genes in the three exon-expression groups: high, medium, and low. (D) Median values and interquartile ranges of the exon average signals in the exon-expression groups high, medium, and low in Class 1 (H3K36me3, H3K79me1, and H2BK5me1), Class 2 (H3K27me2 and H3K27me3), and Class 3 (H3K27me1). Significant differences in distributions were tested for the high/medium- and low/medium-expression groups. An asterisk below or above the interquartile ranges indicates significantly (Wilcoxon rank sum test P-value < 10⁻⁵) lower or greater signal distribution compared to medium-expressed exons.