Qualitative and Quantitative Polymerase Chain Reaction-Based Methods for DNA Methylation Analyses

DNA methylation can be analyzed easily by qualitative or quantitative polymerase chain reaction (PCR)-based methods, including methylation-specific PCR (MSP), bisulfite sequencing, methylation-sensitive restriction enzyme PCR, combined bisulfite restriction analysis (COBRA), methylation-sensitive single nucleotide primer extension (Ms-SNuPE), and quantitative real-time MSP. MSP, which couples the bisulfite modification of DNA and PCR, is fast, highly sensitive, specific, and widely applied for DNA methylation analyses. Bisulfite modification converts unmethylated cytosine to uracil, whereas methylcytosine remains unmodified. Most of these methods require specific PCR primers that are designed to distinguish between methylated and unmethylated DNA sequences. Bisulfite sequencing is comparatively time-consuming. Methylation-sensitive restriction enzyme PCR combines methylation-sensitive restriction enzyme digestion and PCR. After enzyme digestion, PCR products are obtained if the enzyme does not digest the methylated CpG sites within the specified DNA region. COBRA, Ms-SNuPE, and quantitative real-time MSP allow the quantitative analyses of DNA methylation.