Application of Microarrays for DNA Methylation Profiling
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 .
KeywordsDNA methylation microarrays epigenetic profiling epigenetic biomarkers whole genome approach epigenetics
We thank Professor Bernhard Horsthemke for providing DNA samples of Prader-Willi and Angelman syndrome patients and Dr. Jon Mill and Carolyn Ptak for their critical reading of the manuscript.
- 2.2. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern,D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308:1149–1154CrossRefPubMedGoogle Scholar
- 7.7. Li J, Protopopov A, Wang F, Senchenko V, Petushkov V, Vorontsova O, Petrenko L, Zabarovska V, Muravenko O, Braga E, Kisselev L, Lerman MI, Kashuba V, Klein G, Ernberg I, Wahlestedt C, Zabarovsky ER (2002) NotI subtraction and NotI-specific microarrays to detect copy number and methylation changes in whole genomes. Proc Natl Acad Sci USA 99:10724–10729CrossRefPubMedGoogle Scholar
- 8.Schumacher A, Friedrich P, Schmid J, Ibach B, Eisele T, Laws SM, Foerstl H, Kurz A, and Riemenschneider M (2006) No association of chromatin-modifying protein 2B with sporadic frontotemporal dementia. Neurobiol Aging Sep 14 (e-pub ahead of print)Google Scholar