Application of Microarrays for DNA Methylation Profiling

Abstract

Comprehensive analyses of the human epigenome may be of critical importance in understanding the molecular mechanisms of complex diseases, development, aging, tissue specificity, parental origin effects, and sex differences, among other systemic aspects of human biology. However, traditional DNA methylation methods allowed for screening of only relatively short DNA fragments. The advent of microarrays has provided new possibilities in DNA methylation analysis, because this technology is able to interrogate a very large number of loci in a highly parallel fashion. There are several permutations of the microarray application in DNA methylation profiling, and such include microarray analysis of bisulfite modified DNA and also the enriched unmethylated or hypermethylated DNA fractions using methylation-sensitive restriction enzymes or antibodies against methylated cytosines. The method described in detail here is based on the analysis of the enriched unmethylated DNA fraction, using a series of treatments with methylation-sensitive restriction enzymes, adaptor ligation, PCR amplification, and quantitative mapping of unmethylated DNA sequences using microarrays. The key advantages of this approach are the ability to investigate DNA methylation patterns using very small DNA amounts and relatively high informativeness in comparison to the other restriction-enzyme- based strategies for DNA methylation profiling [1].

A Sustained Dietary Change Increases Epigenetic Variation in Isogenic Mice

“…Methyl donors have been reported to induce epigenetic changes in at least two discrete loci ( A vy and Axin Fu ) [5], [12] but it is not known if other genomic loci are also affected. To determine whether methyl donors exert epigenetic changes at other loci, and to resolve the extent of any changes, we compared genomic methylation patterns of supplemented and unsupplemented mice using a recently described method that combines enrichment of the unmethylated fraction of DNA with promoter microarray analysis [24]. Enrichment of the unmethylated fraction gives a better signal-to-noise ratio than other methods based on enrichment of methylated DNA, because removal of most repetitive sequences reduces the size of the DNA pool; moreover, since unmethylated CpG dinucleotides are less abundant in the genome than methylated CpG dinucleotides, this method is considerably more sensitive to DNA methylation changes at CpG islands [25].…”

“…We constructed libraries enriched for the unmethylated fraction of genomic DNA from liver using sequential HpaII and McrBC digestion and ligation-mediated PCR [24], and hybridised them to Agilent Mouse CpG Island 105K arrays representing approximately 16,000 CpG islands. We chose to examine CpG islands for two reasons: first, methylation changes at CpG islands are more likely to reflect regulatory changes than methylation changes at low-CpG density loci [26]; second, the enzymatic enrichment method we used preferentially targets CpG islands.…”

Rethinking Periodontal Inflammation

“…Technology is available to determine genomic‐wide epigenetic changes 26 that can be applied to study tissues at the biofilm interface to compare diseased tissue to healthy control tissue. Such microarray technology 33 may prove successful for identifying a number of hypermethylated and hypomethylated genes associated with periodontal infection (data not shown). For example, preliminary findings suggested that the gene for IL‐6, encoding a cytokine involved in the final differentiation of B cells into immunoglobulin‐secreting cells, undergoes a decrease in methylation (hypomethylation) in periodontal disease tissues compared to control samples (unpublished data).…”

Studying the epigenome using next generation sequencing

“…In comparison, methods that rely on affinity enrichment using antibodies are biased towards enrichment of sites containing relatively high levels of cytosine methylation, namely, CpG islands. These methods were coupled with microarray based methods to enable genome-wide analysis of DNA methylation and histone modifications based on the ChIP-chip method 27 31 39 40…”