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  • DNA Methylation Analysis

    Methods to analyze DNA methylation, DNA demethylation, and their functional effects are critical to epigenetics researchers. Methylation profiles of epigenome are used for disease identification and for research and therapeutic development. Analysis can be gene-specific or global depending on downstream applications (1).

    Downstream methylation detection methods include end-point PCR, real-time PCR, primer extension, single-stranded conformational polymorphism assays, blotting, microarray analysis and sequencing. Choosing which method(s) to use largely depends on the experimental sample size and the goals of the experiments.


    1. Tao Zuo et al. 2009, Epigenomics  1(2) 331-345. PMID: 20526417
    1. What Is Epigenetics?

      If all cells are created from the same genetic material, why are there so many different cell types? Listen to Sriharsa Pradhan, Research Division Head, RNA Biology at NEB, as he describes how DNA is methylated and how this affects the path of reading the DNA code the same way an obstruction would derail a train off its tracks.

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    DNA Methylation Analysis includes these areas of focus:

    5-hmC Detection & Analysis
    Methylated DNA Analysis
    Bisulfite Conversion

    FAQs for DNA Methylation Analysis

    Protocols for DNA Methylation Analysis

    Methods of DNA Methylation Analysis

    • Bisulfite conversion, which provides single nucleotide, high resolution data for whole genomes or single locus methylation studies.
    • Differential enzymatic cleavage, which uses methylation, or dually 5-mC and 5-hmC dependent enzymes, paired with non-sensitive isoschizomers to asses DNA methylation or DNA hydroxymethylation.
    • High-Performance Liquid Chromatography (HPLC)
    • Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry(MALDI-TOF MS)
    • Methylated DNA-ELISA
    • Affinity-based methods, which use methylated DNA binding proteins or antibodies for enrichment.
    • Enzymatic DNA methyltransferase assay