A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements

• DOI: 10.1093/nar/gnh032
• Publication Date: 2004-02-20T21:23:22Z
• Authors: A. S. Yang
• Keywords: Illumina Methylation Assay; Bisulfite sequencing; Methylated DNA immunoprecipitation; Alu element; CpG site; genomic DNA; Pyrosequencing; Bisulfite; RNA-Directed DNA Methylation; Primer (cosmetics)

We report a method for studying global DNA methylation based on using bisulfite treatment of and simultaneous PCR multiple repetitive elements, such as Alu elements long interspersed nucleotide (LINE). The product, which represents pool approximately 15 000 genomic loci, could be used direct sequencing, selective restriction digestion or pyrosequencing, in order to quantitate methylation. By the assay was reproducible with standard deviation only 2% between assays. Using this we found that almost two‐thirds CpG sites are mutated, but remaining target sites, 87% were methylated. Due heavy especially useful detecting decreases methylation, validated by examining cell lines treated inhibitor 5‐aza‐2′deoxycytidine (DAC), where 1–16% decrease element 18–60% LINE within 3 days treatment. This can surrogate marker genome‐wide changes. In addition, it is less labor intensive requires than previous methods assessing