Comprehensive high‑throughput arrays for relative methylation (CHARM)

Cited from the paper "Comprehensive High-Throughput Arrays for Relative Methylation (CHARM)"

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Overview of McrBC-based fractionation (Lippman et al., 2005; Ordway et al., 2006) coupled with CHARM analysis (Irizarry et al., 2008). Genomic DNA is sheared to 1.5 to 3.0 kb and divided into two equal parts. The first is digested with McrBC, a methyl-cytosine insensitive enzyme that recognizes PumC(N40–3000)mCPu, and the second is untreated. Both fractions are then resolved side by side on a 1% agarose gel, and fragments between 1.65 kb and 3.0 kb are excised and purified. Next, the untreated fraction, representing total input DNA, is labeled with cyanine-3 (Cy3) and the McrBC-treated fraction, representing unmethylated DNA, is labeled with cyanine-5 (Cy5) followed by cohybridization to a CHARM microarray. Sequences that are methylated will be present in the input fraction (Cy3) and depleted in the methyl-depleted fraction (Cy5). For each probe on the array, a log ratio of the Cy3 to Cy5 intensity is calculated and represents the methylation level (M-value) at each locus, with larger M-values representing more methylation and smaller M-values representing less methylation.
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Cited from the paper "Profiling genome-wide DNA methylation"
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McrBC, an  enzyme that digests methylated DNA, to fractionate DNA  and subsequently utilizes array hybridization. 
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