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Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias


Background: DNA methylation primarily occurs at CpG dinucleotides in mammals and is a common epigenetic mark that plays a critical role in the regulation of gene expression. Profiling DNA methylation patterns across the genome is vital to understand DNA methylation changes that occur during development and in disease phenotype. In this study, we compared two commonly used approaches to enrich for methylated DNA regions of the genome, namely methyl-DNA immunopreciptation (MeDIP) that is based on enrichment with antibodies specific for 5?-methylcytosine (5MeC), and capture of methylated DNA using a methyl-CpG binding domain-based (MBD) protein to discover differentially methylated regions (DMRs) in cancer. Results: The enriched methylated DNA fractions were interrogated on Affymetrix promoter tiling arrays and differentially methylated regions were identified. A detailed validation study of 42 regions was performed using Sequenom MassCLEAVE technique. This detailed analysis revealed that both enrichment techniques are sensitive for detecting DMRs and preferentially identified different CpG rich regions of the prostate cancer genome, with MeDIP commonly enriching for methylated regions with a low CpG density, while MBD capture favours regions of higher CpG density and identifies the greatest proportion of CpG islands. Conclusions: This is the first detailed validation report comparing different methylated DNA enrichment techniques for identifying regions of differential DNA methylation. Our study highlights the importance of understanding the nuances of the methods used for DNA genome-wide methylation analyses so that accurate interpretation of the biology is not overlooked.

Authors Nair, S., Coolen, M.W., Stirzaker, C., Song, J., Statham A.L., Strbenac, D., Robinson, M.D.; Clark S.J.
Responsible Garvan Author Dr Shalima Nair
Publisher Name Epigenetics
Published Date 2011-03-01
Published Volume 6
Published Issue 1
Published Pages 34-44
Status Published in-print
URL link to publisher's version
OpenAccess link to author's accepted manuscript version