Figure 2

Exonic DNA methylation and nucleosome occupancy. (a) Nucleosome occupancy (upper panel) and CpG methylation (lower panel) plotted as the average of all transcripts across non-coding exons (NCEs), coding exons, and flanking introns according to their relative positions within the transcript. All exons and introns were partitioned into ten bins and the average normalized read count (NRC) was obtained for each bin of all corresponding exons and introns. ICEs (initial coding exons) and LCEs (last coding exons) are broken into the UTR (light blue or light green) and coding region (dark blue or dark green) by the start codon and stop codon, respectively. The ends of the introns (orange) are connected to those of the flanking exons by the black lines. (b) Exon inclusiveness measured as the relative expression of each internal exon compared to the other exons in the transcript. The lowest 10% were considered spliced out and the others to be spliced in. The top 10% were identified as highly expressed for the purpose of checking for sequencing bias. (c) Comparison of nucleosome occupancy (upper panel) and CpG methylation (lower panel) among skipped exons, included exons, and highly expressed exons as defined above. tss, transcriptions start site.