Microarray-based DNA methylation profiling: technology and applications

Abstract

This work is dedicated to the development of a technology for unbiased, high-throughput DNA methylation profiling of large genomic regions. In this method, unmethylated and methylated DNA fractions are enriched using a series of treatments with methylation sensitive restriction enzymes, and interrogated on microarrays. We have investigated various aspects of the technology including its replicability, informativeness, sensitivity and optimal PCR conditions using microarrays containing oligonucleotides representing 100 kb of genomic DNA derived from the chromosome 22 COMT region in addition to 12 192 element CpG island microarrays. Several new aspects of methylation profiling are provided, including the parallel identification of confounding effects of DNA sequence variation, the description of the principles of microarray design for epigenomic studies and the optimal choice of methylation sensitive restriction enzymes. We also demonstrate the advantages of using the unmethylated DNA fraction versus the methylated one, which substantially improve the chances of detecting DNA methylation differences. We applied this methodology for fine-mapping of methylation patterns of chromosomes 21 and 22 in eight individuals using tiling microarrays consisting of over 340 000 oligonucleotide probe pairs. The principles developed in this work will help to make epigenetic profiling of the entire human genome a routine procedure.

Prospects for Epigenetic Epidemiology

“…DNA methylation can also be studied on a genome-wide scale using a variety of enzyme-based or antibody affinity techniques that enrich for either methylated or unmethylated fractions of genomic DNA (157)(158)(159)(160)(161)(162). These fractions can then be hybridized to DNA microarrays or sequenced en masse.…”

Towards defining the lymphoma methylome

“…15 However, this methodology is currently limited to the analysis of candidate loci. To overcome this limitation, recent efforts have focused on global epigenomic approaches, which have led to the development and application of a number of different techniques exploiting the potential of microarray technologies [16][17][18][19][20][21][22] (reviewed by Callinan and Feinberg 23 ). In this context, Rahmatpanah and co-workers describe the application of a CpG-island microarray for the genome-wide characterization of DNA methylation profiles in mantle cell lymphomas (MCLs), B-cell chronic lymphocytic leukemias/ small lymphocytic lymphomas (B-CLLs/SLLs) and low-grade follicular lymphomas (FLs).…”

“…Therefore, not all the CpG-islands in the genome can be interrogated. 20 An alternative to this approach is the immunoprecipitation of methylated DNA with an antibody against 5-methyl-cytosine (MeDIP technique). 21 In MeDIP assays, input DNA (i.e.…”

Not really identical: Epigenetic differences in monozygotic twins and implications for twin studies in psychiatry

“…Kaminsky et al mapped differences in DNA methylation at a locus displaying a range of co-twin variability in three types of tissues-white blood cells, buccal epithelial cells, gut (rectum) biopsies and-from MZ and DZ twin pairs using microarrays [Schumacher et al, 2006]. They found a large degree of MZ co-twin DNA methylation variation in all the tissue samples investigated, validating their findings using sodium bisulfite modification based mapping of methylated cytosines in CpG islands [Frommer et al, 1992;Kaminsky et al, 2009].…”