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Restriction site-specific methylation studies of imprinted genes with quantitative real-time PCR. | LitMetric

AI Article Synopsis

  • Epigenetic studies focus on DNA methylation to better understand syndromes related to imprinted genes, which can aid in diagnostics.
  • The research method involved digesting DNA with specific enzymes and using quantitative real-time PCR to analyze imprinting control regions, particularly in individuals with uniparental disomy of chromosome 7 (UPD7).
  • Results showed strong correlation between expected and observed methylation levels in UPD7 cases and control samples, indicating that the technique offers a reliable way to assess methylation changes, which can be applied to diagnose conditions like Silver-Russell and Beckwith-Wiedemann syndromes.

Article Abstract

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 lambda 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.

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Source
http://dx.doi.org/10.1373/clinchem.2007.098491DOI Listing

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