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Restriction Site–Specific Methylation Studies of Imprinted Genes with Quantitative Real-Time PCR

¹ Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden;² Department of Medical Genetics, University of Helsinki, Helsinki, Finland;³ Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK;⁴ Oxford Centre for Diabetes, Endocrinology and Medicine, University of Oxford, Churchill Hospital, Oxford, UK;⁵ Hospital for Children and Adolescents, University of Helsinki, Helsinki, Finland.

^aAddress correspondence to this author at: Department of Biosciences and Nutrition, Hälsovägen 7-9, 14157 Huddinge, Sweden. Fax 46-8-7745538; e-mail sara.bruce{at}biosci.ki.se.

Background: Epigenetic studies, such as the measurement of DNA methylation, are important in the investigation of syndromes influenced by imprinted genes. Quick and accurate quantification of methylation at such genes can be of appreciable diagnostic aid.

Methods: We first digested genomic DNA with methylation-sensitive restriction enzymes and used DNA without digestion as a control and nonmethylated DNA as an internal control for digestion efficiency. We then performed quantitative real-time PCR analyses with 6 unique PCR assays to investigate 4 imprinting control regions on chromosomes 7 and 11 in individuals with uniparental disomy of chromosome 7 (UPD7) and in control individuals.

Results: Our validation of the method demonstrated both quantitative recovery and low methodologic imprecision. The imprinted loci on chromosome 7 behaved as expected in maternal UPD7 (100% methylation) and paternal UPD7 (<10% methylation). In controls, the mean (SD) for percent methylation at 2 previously well-studied restriction sites were 46% (6%) for both H19 and KCNQ1OT1, a result consistent with the previously observed methylation rate of approximately 50%. The methylation percentages of all investigated imprinted loci were normally distributed, implying that the mean and SD can be used as a reference for screening methylation loss or gain.

Conclusion: The investigated loci are of particular importance for investigating the congenital Silver–Russell and Beckwith–Wiedemann syndromes; however, the method can also be applied to other imprinted regions. This method is easy to set up, has no PCR bias, requires small amounts of DNA, and can easily be applied to large patient populations for screening the loss or gain of methylation.