DNA methylation arrays are the definition of workhorses: they may be older, but they are tried and true and still get the job done. Methylation arrays are designed to work with other techniques. HELP, bisulfite, MeDIP and just about any other technique can utilize microarray technology.
A main advantage of microarrays in methylation studies is they can be targeted to methylated or potentially methylated regions (Gitan et al., 2002). CpG island arrays for example target all known CpG islands. Promoter arrays are also very common, they typically cover all refeq promoters of the species (human, mouse or rat) of interest. The Illumina 450k infinium methylation beadchip is one of the most common chips used in human methylation research. It covers 96% of CpG islands, >99% promoters, non-CpG methylated sites, and miRNA promoters (more info here).
Microarrays have been out-paced by sequencing in almost all metrics (Meaburn and Schulz, 2012); however, microarray use is still alive and well. This is because of the low cost, high-throughput nature of arrays. Methylation arrays are still very much is use to compliment or kick-off larger projects or perform large-scale, high throughput experiments.
DNA Methylation Arrays Additional Reading
This paper offers an empirical examination of the function of the 450k infinium beadchip. In addition to giving a good description of the basic technology, the authors provide description and evaluation of each step of the workflow and analysis.
- Gitan, R., Shi, H., Chen, C., Yan, P., and Huang, T. (2002). Methylation-specific oligonucleotide microarray: A new potential for high-throughput methylation analysis. Genome Res. 12, 158-164.
- Meaburn, E., and Schulz, R. (2012). Next generation sequencing in epigenetics: insights and challenges. Semin. Cell Dev. Biol. 23, 192-199.