Fig. 3

Validation and extended mapping for the differentially methylated genes HAND2, RBMS1, HIST1H3E, and PAX3. Bisulfite cloning sequencing experiments show that hypermethylation affects multiple contiguous CpGs located in the 3’UTR of HAND2 (a), first exon of RBMS1 (b), the promoter region of HIST1H3E (c), and the body of PAX3 (d). The upper track of each panel shows a genomic map of each gene. White boxes below each gene denote CpG islands, and black boxes represent bisulfite cloning sequencing amplicons. Dot plot graphs show the results of the 450K array (beta values) for CpG probes. Validation results are represented by black/white circle-style figures. Each rectangle corresponds to one sample and shows the methylation pattern at a discrete genomic region surrounding the significant CpG probed by the 450K array which is marked by a red arrow. Black circles represent methylated cytosines while white circles denote unmethylated cytosines. Each column symbolizes a unique CpG site in the examined amplicon, and each line represents an individual DNA clone. Average percentage of methylation for each analyzed sample (control or patient) at this particular amplicon is indicated at the bottom of each sample