Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation
- Mark D. Robinson1,2,
- Clare Stirzaker1,
- Aaron L. Statham1,
- Marcel W. Coolen1,3,
- Jenny Z. Song1,
- Shalima S. Nair1,
- Dario Strbenac1,
- Terence P. Speed2 and
- Susan J. Clark1,4,5
- 1 Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia;
- 2 Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne 3052, Victoria, Australia;
- 3 Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6500 HB Nijmegen, The Netherlands;
- 4 St. Vincent's Clinical School, University of New South Wales, Sydney 2010, New South Wales, Australia
Abstract
DNA methylation is an essential epigenetic modification that plays a key role associated with the regulation of gene expression during differentiation, but in disease states such as cancer, the DNA methylation landscape is often deregulated. There are now numerous technologies available to interrogate the DNA methylation status of CpG sites in a targeted or genome-wide fashion, but each method, due to intrinsic biases, potentially interrogates different fractions of the genome. In this study, we compare the affinity-purification of methylated DNA between two popular genome-wide techniques, methylated DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain-based capture (MBDCap), and show that each technique operates in a different domain of the CpG density landscape. We explored the effect of whole-genome amplification and illustrate that it can reduce sensitivity for detecting DNA methylation in GC-rich regions of the genome. By using MBDCap, we compare and contrast microarray- and sequencing-based readouts and highlight the impact that copy number variation (CNV) can make in differential comparisons of methylomes. These studies reveal that the analysis of DNA methylation data and genome coverage is highly dependent on the method employed, and consideration must be made in light of the GC content, the extent of DNA amplification, and the copy number.
Footnotes
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↵5 Corresponding author.
E-mail s.clark{at}garvan.org.au; fax 61-2-92958316.
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[Supplemental material is available online at http://www.genome.org. The data from this study have been submitted to Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under SuperSeries accession no. GSE24546.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.110601.110.
- Received May 18, 2010.
- Accepted September 23, 2010.
- Copyright © 2010 by Cold Spring Harbor Laboratory Press