DNA Methylation: A Timeline of Methods and Applications

Abstract

DNA methylation is a biochemical process where a DNA base, usually cytosine, is enzymatically methylated at the 5-carbon position. An epigenetic modification associated with gene regulation, DNA methylation is of paramount importance to biological health and disease. Recently, the quest to unravel the Human Epigenome commenced, calling for a modernization of previous DNA methylation profiling techniques. Here, we describe the major developments in the methodologies used over the past three decades to examine the elusive epigenome (or methylome). The earliest techniques were based on the separation of methylated and unmethylated cytosines via chromatography. The following years would see molecular techniques being employed to indirectly examine DNA methylation levels at both a genome-wide and locus-specific context, notably immunoprecipitation via anti-5′methylcytosine and selective digestion with methylation-sensitive restriction endonucleases. With the advent of sodium bisulfite treatment of DNA, a deamination reaction that converts cytosine to uracil only when unmethylated, the epigenetic modification can now be identified in the same manner as a DNA base-pair change. More recently, these three techniques have been applied to more technically advanced systems such as DNA microarrays and next-generation sequencing platforms, bringing us closer to unveiling a complete human epigenetic profile.

Aberrant DNA methylation in melanoma: biomarker and therapeutic opportunities

“…Alternative approaches of focused differential methylation analysis include enriching for a subpopulation of DNA recognized by antibodies against 5-methylcytosine (MeDIP) or “pulling down” DNA using methyl-binding proteins (MBD-Seq) before sequencing. Comprehensive comparisons of currently available techniques and considerations regarding their use are available in literature [10, 12, 13]. …”

Make way for the ‘next generation’: application and prospects for genome-wide, epigenome-specific technologies in endocrine research

“…For a comprehensive timeline of methods and applications, the reader is directed to recent excellent reviews (Baylin & Jones 2011, Harrison & Parle-McDermott 2011. However, it was not until 1992 that a now classic paper described the sodium bisulphite conversion technique, which when combined with conventional dideoxy sequencing allowed, for the first time, the analysis of DNA methylation patterns in genomic DNA (Frommer et al 1992).…”

“…These analyses rely on chromatin immunoprecipitation (ChIP) of specific histone tail modification and subsequent quantitative PCR of enriched, gene-specific DNA fragments. Antibody-mediated enrichment strategies, for either histone modification (ChIP) or DNA methylation, as example, methylated DNA immunoprecipitation (MeDIP), may also be used in combination with DNA tiling or CpG island promoter arrays (ChiP-Chip) for genome-wide analyses (reviewed in Harrison & Parle-McDermott (2011) and discussed in a subsequent section). However, a drawback of these techniques for the characterisation of change in DNA methylation is their inability to pinpoint DNA methylation at single-base-pair resolution (Beck & Rakyan 2008).…”

A refined DNA methylation detection method using MspJI coupled quantitative PCR

“…The gold standard method for DNA methylation measurement is sodium bisulfite conversion. In this method, sodium bisulfite reacts with unmethylated cytosines, and converts them to uracil, whereas the methylated cytosines are not affected [11,12]. Combined with whole genome sequencing, bisulfite conversion provides a high-resolution map of the DNA methylation at a single cytosine level for the entire genome.…”