Figure 6

Polymorphic genomic region between BP1 and BP2 revealed by PFGE analysis. A. A Not I restriction enzyme map of the 15q11-q13 region revealed by computational analysis. There are total of 15 Not I sites identified and labeled as N1 to N15. N5 and N7–N9 were known to be differentially methylated with absence of methylation of the paternal allele and methylation of the maternal allele [9, 23, 68, 69] The known genes associated with Not I are diagramed below the line and the BAC clones where the Not I sites are mapped are shown. P1–P5 are genomic DNA probes used for PFGE analysis. B1-5. The result of PFGE analysis using Not I and genomic DNA probes P1–P5. The DNAs are from PWS and AS patients with large class I deletions. The pattern is consistent with allele-specific differential methylation of the Not I sites associated with SNRPN (N7-9) and MKRN3 (N5), methylation of both alleles for C15orf2 as previously reported, and the absence of methylation for the remainder of the Not I sites in the region. C1-5. The results of PFGE analysis using Not I and probes P1–P5 in normal individuals. The extensive variation revealed by probes P1 and P2 indicate a polymorphic genomic region between BP1 and BP2. The pattern of two bands shown in panel C3 using probe P3 is consistent with allele-specific differential DNA methylation of the Not I sites within the SNRPN CpG island (N7–N9). The lower band represents a genomic fragment (~500 kb) from the paternal chromosome between the CpG island of SNRPN and the CpG island of UBE3A.