Figure 5

Non-CG cytosine modifications might affect alternative mRNA splicing. a, top blue lines indicated alternatively spliced exons in AHB and EHB. Underneath the exon sequences are the BS-Seq results showing the locations of CpG, CHG, and CHH ^mC sites. Note that ^mC in an exon correlates with the skipping of the exon by alternative splicing. For example, the gene GB15706, which encodes a homolog to Chromatin assembly factor 1 subunit A (CAF1A), has heavy CpG, CHH, and CHG methylation in a downstream exon that is skipped in AHB and present in EHB. Conversely, this gene has heavy cytosine methylation in the upstream exon in EHB that is skipped in EHB but present in AHB. Details of the RNA-seq analyses is in Additional file1: Figure S7. b, Top blue lines indicated alternatively spliced exons in AHB and EHB, The red-and-blue stacked lines underneath the exons show Pvu-Seq analyses of AHB and EHB heads. Note that ^hmC also correlates with alternative mRNA splicing, but in manners that differ from ^mC (see text). Details of the RNA-seq analyses are given in Additional file1: Figure S7.