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Table 2 Technologies to identify genome-wide epigenetically regulated genes

From: Epigenetics of renal cell carcinoma: the path towards new diagnostics and therapeutics

Method Key features Advantages Disadvantages
Functional epigenomics Methylated genes are re-expressed in cell lines by treatment with 5-aza-2'-deoxycytidine. Expression arrays determine reactivated genes Links hypermethylated sites to gene silencing Correlating correct methylated site to expression regulation is laborious. Cell lines are frequently more methylated than the corresponding tumors.
Methylation-dependent immunoprecipitation
Methylated DNA is separated from unmethylated DNA by immunoprecipitation and hybridized to a CpG island microarray Global analysis; produces quantifiable results Dependent on good immunoprecipitation efficiency;
difficult to determine the extent of methylation across a specific CpG island
Bead chip
Bisulfite-modified DNA is hybridized to beads containing DNA oligonucleotides specific to CpG dinucleotide methylation. Single base extension determines methylation state Global analysis at single CpG sites using targeted probes;
quantitative data
Provides data for only one or two CpG dinucleotides per island; further work may be required to determine the extent of methylation at specific sites
Next-generation sequencing Combines isolation of methylated DNA using techniques such as MeDIP or restriction digest and high-throughput sequencing. Bisulfite-modified DNA can also be sequenced directly Statistically robust; high coverage; single nucleotide resolution Initial set-up costs high; probe design can be challenging