Methods of the genome-wide DNA methylation analysis

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Methods of genome-wide screening for differences in DNA methylation consist of two steps, detection of DNA methylation and genome-wide screening. DNA methylation statuses can be detected based on several principles, affinity to methylated DNA, such as an anti-5-methylcytocine antibody, methylation-sensitive restriction enzymes, bisulfite conversion reaction, and induction of gene expression by treatment with a demethylating agent. Genome-wide screening can be conducted by several methods, such as microarray, next-generation deep sequencer, two-dimensional electrophoresis, and DNA subtraction. These methods have quite different versatility of resolution, quantitativity, cost-effectiveness, and necessary instruments.

For example, methylated DNA immunoprecipitation-microarray analysis (MeDIP microarray) is a method using immunoprecipitation of methylated DNA by an antibody of 5-methylcytocine and oligonucleotide microarray. At present, the MeDIP microarray has reasonable resolution, quantitativity and cost-effectiveness. Methylation-sensitive representational difference analysis (MS-RDA) is a method using methylation-sensitive restriction enzymes and DNA subtraction. This method is inferior to methods involving microarray in resolution and simpleness of procedure, but even now, has an advantage in an application to the species whose genome sequences are not available. If one wants to identify methylation-silenced genes and a cell line is available, expression microarray screening of genes re-expressed after treatment of the cell line with a demethylating agent is effective.