Fig. 1

Schematic diagram showing the location of PAX3 region analyzed. a Locations of the CpG sites detected in phase 1 and phase 2 of human methylation analysis. The differentially methylated CpG units identified by HM450K were indicated as white dots that above the black line (cg19352038, cg08022524, cg04407305, cg25809290, cg23077820, cg11490745, and cg04134754). In phase 2, three DNA amplicons were developed to validate the differentially methylated region detected in phase 1; amplicon 1 covered 10 analytical CpG sites located in the TSS1500 region of PAX3; amplicon 2 covered 16 analytical CpG sites located between TSS200 and 5′UTR region; amplicon 3 covered 9 analytical CpG sites located between the 4th and 5th exon. All the CpG sites detected in replication phase were indicated as black dots under the line. b Locations of the Pax3 CpG sites detected in mouse methylation analysis. Three DNA amplicons were developed as in human study. Amplicon 1 covered 8 analytical CpG sites located in the TSS1500 region of Pax3; amplicon 2 covered 7 analytical CpG sites which located between TSS200 and 5′UTR region; amplicon 3 covered 12 analytical CpG sites located between the 4th and 5th exon. c Schematic diagram of interest indicating putative transcription factor-binding sties in amplicon 3 of human PAX3 gene in intron 4. CpG sites predicted by JASPAR (predictive value > 8) to bind transcription factors are described under the sequence. CpG site 3 was the same as cg23077820 identified differentially by HM450K in phase 1. All the CpG sites except CpG site 12 were differentially methylated between NTDs and controls by Sequenom EpiTYPER in phase 2