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The HELP assay.

Mayumi Oda1, John M Greally

  • 1Departments of Medicine (Hematology) and Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.

Methods in Molecular Biology (Clifton, N.J.)
|November 7, 2008
PubMed
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The HELP assay positively identifies hypomethylated DNA regions, unlike other methods. This technique uses HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) to accurately map DNA methylation patterns genome-wide.

Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Ligation-mediated PCR generates genomic representations for high-throughput assays.
  • Cytosine methylation is a key epigenetic modification studied in the genome.
  • Existing methylation assays infer hypomethylation by signal absence, which can be unreliable.

Purpose of the Study:

  • To introduce and validate the HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) assay.
  • To enable positive representation of hypomethylated DNA.
  • To accurately discriminate between methylated and hypomethylated DNA loci.

Main Methods:

  • Generating genomic representations using ligation-mediated PCR.
  • Utilizing HpaII enzyme for enrichment of specific DNA fragments.

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  • Employing comparative genomic hybridization with MspI representation.
  • Discriminating loci based on representation by HpaII and MspI.

    • Main Results:

    • The HELP assay provides a positive readout for hypomethylated DNA.
    • It distinguishes hypomethylated loci (represented by both HpaII and MspI) from methylated loci (represented by MspI only).
    • This method overcomes confounding technical issues associated with indirect detection of hypomethylation.

    Conclusions:

    • The HELP assay is a robust method for studying DNA cytosine methylation.
    • It offers a more accurate approach to identifying hypomethylated regions, which are functionally significant.
    • This technique advances high-throughput analysis of epigenetic modifications.