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A deletion of 15q11-q13 and uniparental disomy 15 lead to Prader-Labhart-Willi syndrome (PWS) or Angelman syndrome (AS) because this region contains genes expressed exclusively from the paternal (PWS) or maternal (AS) chromosome, respectively. DNA methylation plays a role in the control of imprinted gene expression, but so far only a few 5′-CG-3′ dinucleotides within the recognition sites of the methylation sensitive enzymes have been studied. As part of a study on DNA methylation patterns in the human genome, we have applied the bisulfite protocol of genomic sequencing to study all 5′-CG-3′ dinucleotides around exon 1 of  SNRPN  and at the  D15S63  locus, which contains a start site for alternative  SNRPN  transcripts possibly involved in imprint switching during gametogenesis. At least 17 PCR products derived from single chromosomes of normal individuals as well as PWS and AS patients have been sequenced. We have found that cytosine residues outside 5′-CG-3′ dinucleotides are always unmethylated. However, &gt;96% of all of the 23 5′-CG-3′ dinucleotides around  SNRPN  exon 1 are methylated on the maternal chromosome and completely devoid of methylation on the paternal chromosome. This finding is in contrast to the  D15S63  locus, where only the two  Cfo I/ Hha I sites are methylated on the maternal chromosome at the same frequency as seen for the  SNRPN  segment. At the other five 5′-CG-3′ dinucleotides, differential methylation is less pronounced, i.e. 45–70% on the maternal chromosome and 5–14% on the paternal chromosome. The differences between  SNRPN  and  D15S63  methylation may reflect different biological functions of the alternative  SNRPN  transcripts. The systematic investigation of 5′-CG-3′ methylation patterns as reported here will provide the basis for a PCR-based methylation test to diagnose PWS and AS.

human molecular genetics

Imprinted Segments in the Human Genome: Different Dna Methylation Patterns in the Prader-Willi/Angelman Syndrome Region As Determined by the Genomic Sequencing Method