MRE-Seq, MeDIP, MBD-seq, RRBS and MethylC-seq/BS-seq/WGBS

MeDIP (Methylated DNA immunoprecipitation), methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq) and MethylC-seq/BS-seq/WGBS (bisulfite sequencing) are reviewed in Mapping Human Epigenomes

"The DNA methylation toolkit includes three main molecular-biology-based techniques: digestion of genomic DNA with methyl-sensitive restriction enzymes, affinity-based enrichment of methylated DNA fragments, and chemical conversion methods."

"Affinity-based enrichment assays capture methylated fragments from sonicated DNA with an antibody (MeDIP-seq) or a methyl-binding domain (MBD-seq) (Down et al., 2008 and Serre et al., 2010). When sequencing enriched DNA fragments, at least one cytosine is certainly methylated but the exact site or combination of sites can not be directly determined. Therefore, the resolution of affinity-based assays is highly dependent on the DNA fragment size, CpG density, and immunoprecipitation quality of the reagent. The results of both restriction-enzyme- and affinity-based sequencing methods are qualitative levels of enrichment rather than absolute."

"Bisulfite sequencing is a chemical conversion method that directly determines the methylation state of each cytosine in a binary fashion and is widely accepted as a gold standard for mapping DNA methylation. Treatment of genomic DNA with sodium bisulfite chemically converts unmethylated cytosines to uracil. After PCR, and assuming nearly complete bisulfite conversion, all unmethylated cytosines become thymidines and remaining cytosines correspond to 5mC."