Figure 3

Prominent hmC changes mark the exon-intron boundary. (a, b) Profiles of hmC and mC for a 40-bp window around the exon-intron and intron-exon boundaries at single-nucleotide resolution in human (a) and mouse (b). Modification levels of hmC, mC, total DNA methylation (hmC + hmC), and the CpG number are shown for all internal exons in the sense strand. The sequences ± 9 bp around the 5′ and 3′ splicing sites are also indicated. The TAB-Seq and BS-Seq data to generate the mouse profile (b) were obtained from Lister et al.[25]. (c) Profiles of hmC and mC at the exon-intron boundary of exons which have a CpG at 5′ss position -2 (-2CG, n = 8,212) or -1 (-1CG, n = 4,277). Since a CpG at one position will lead to absence of CpG at the nearest neighboring position and thus no methylation value, we merged the data of the sense and the antisense strands for each type of exons. (d) Profiles of hmC and mC across exons. All internal exons were divided into 100 bins, and average hmC and mC levels were calculated for each bin, as well as ±150 bp surrounding the exon. (e) The hmC and mC profiles at the exon-intron boundary of the first exon.