Method of DNA methylation patterns in CpG islands
Method of DNA methylation patterns in CpG islands (or CpG-rich regions of promoter) is crutial as it allows to gather information regarding understanding various biological processes occurring in the cells, for instance, inactivation of X chromosome, regulation of imprinted genes or suppressor gene silencing in tumor cells. Methylation-specific PCR (MSP) is conducted through modification of DNA by sodium bisulfate that converts all unmethylated but not methylated, cytosines (C) to uracil (U) following by amplification with primers that are specific for methylated versus unmethylated DNA. Unlike other PCR-based methods used previously that were relying strictly on differential restriction enzyme cleavage in determining methylated and unmethylated DNA, MSP helps to avoid the false positive results inherent. Thus, MSP is an excellent technique that can be applied in evaluating of the methylation status in CpG island (1). However, it is important to keep in mind that though MSP is flexible when it comes to the selection of a genomic region for analysis (because PCR primers can be designed at arbitrary positions, even if the region to be analyzed is CpG-rich), the optimal number of PCR cycles and annealing temperatures with appropriate negative controls should always be utilized in order to prevent inadequate results
