Measurement of Genome-Wide DNA Cytosine-5 Methylation by Reversed-Phase High-Pressure Liquid Chromatography

In health, approx 4% of cytosines are methylated. Tissues can vary in their levels of DNA methylation and the overall level is often reduced in malignancy (1 ). The level of DNA methylation is usually obtained by chromatographic separation of the constituent nucleotide bases or their related deoxyribonucleotides or deoxyribonucleosides, and is usually represented as a fraction of total cytosine. Quantification of 5mC by chromatographic separation of deoxyribonucleotides has the advantage that, as deoxyribonucleotides can be easily distinguished from ribonucleotides, contamination of the DNA by RNA is less likely to cause error. This can be the case if 5mC is assayed after chemical hydrolysis of the DNA to bases.