Complex Exon-Intron Marking by Histone Modifications Is Not Determined Solely by Nucleosome Distribution
Figure 4
RNA polymerase II (Pol II) occupancy levels are increased at transcribed exons.
a. Pol II levels across consensus expressed (“ON”) (n = 245) and non-expressed (“OFF”) genes (n = 115). b. Histograms show levels of Pol II at 5′ ends and across gene bodies with respect to canonical/alternatively-spliced exons and introns of expressed genes [n = 181, canonical exon:alternatively-spliced exon∶intron = 330∶151∶496 (5′ ends) or 1705/371/2110 (gene bodies)]. Biases favoring either canonical exon or intron are summarized by the difference in Z-scores shown above each assay in grey. Positive (+) differences in Z-scores reflect exon biases, while negative (−) differences reflect intron biases. Error bars are 95% confidence intervals. c. Exon-intron tracking of Pol II across the first ten exons and nine introns of consensus expressed genes (n = 181, exon∶introns = 980∶376) (hypothetical gene structure shown below panel). d. Exon-intron tracking of Pol II across last 5 exons and 4 introns of consensus expressed genes (n = 181, exon∶introns = 563∶148) (hypothetical gene structure shown below panel). Median P-values obtained from bootstrapping for exons and introns in c and d were both <1.0×10−15. Median P-values obtained for pair-wise t-tests between adjacent exon-intron pairs in data from c (exon2 → exon10) and in d (exonslast-4 → exonlast) were 5.06×10−6 and 6.30×10−4 respectively. In all panels, Pol II ChIP-chip enrichments across ENCODE genes in the K562 and U937 cell lines are expressed as mean Z-scores.