MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
- Mattia Pelizzola1,5,
- Yasuo Koga2,5,
- Alexander Eckehart Urban2,
- Michael Krauthammer3,
- Sherman Weissman2,
- Ruth Halaban4, and
- Annette M. Molinaro1,6
- 1 Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520, USA;
- 2 Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA;
- 3 Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA;
- 4 Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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↵5 These authors contributed equally to this work.
Abstract
DNA methylation is an important component of epigenetic modifications that influences the transcriptional machinery and is aberrant in many human diseases. Several methods have been developed to map DNA methylation for either limited regions or genome-wide. In particular, antibodies specific for methylated CpG have been successfully applied in genome-wide studies. However, despite the relevance of the obtained results, the interpretation of antibody enrichment is not trivial. Of greatest importance, the coupling of antibody-enriched methylated fragments with microarrays generates DNA methylation estimates that are not linearly related to the true methylation level. Here, we present an experimental and analytical methodology, MEDME (modeling experimental data with MeDIP enrichment), to obtain enhanced estimates that better describe the true values of DNA methylation level throughout the genome. We propose an experimental scenario for evaluating the true relationship in a high-throughput setting and a model-based analysis to predict the absolute and relative DNA methylation levels. We successfully applied this model to evaluate DNA methylation status of normal human melanocytes compared to a melanoma cell strain. Despite the low resolution typical of methods based on immunoprecipitation, we show that model-derived estimates of DNA methylation provide relatively high correlation with measured absolute and relative levels, as validated by bisulfite genomic DNA sequencing. Importantly, the model-derived DNA methylation estimates simplify the interpretation of the results both at single-loci and at chromosome-wide levels.
Footnotes
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↵6 Corresponding author.
↵6 E-mail annette.molinaro{at}yale.edu; fax (203) 785-6912.
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[Supplemental material is available online at www.genome.org. The microarray data from this study have been submitted to Gene Expression Omnibus (GEO) under accession no. GSE12096. The MEDME R library, installation instructions, and a PDF tutorial are available online at http://espresso.med.yale.edu/medme/.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.080721.108.
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- Received May 10, 2008.
- Accepted July 10, 2008.
- Copyright © 2008, Cold Spring Harbor Laboratory Press
