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Quantitative comparison of genome-wide DNA methylation mapping technologies

Nature Biotechnology volume 28, pages 1106–1114 (2010)Cite this article

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Abstract

DNA methylation plays a key role in regulating eukaryotic gene expression. Although mitotically heritable and stable over time, patterns of DNA methylation frequently change in response to cell differentiation, disease and environmental influences. Several methods have been developed to map DNA methylation on a genomic scale. Here, we benchmark four of these approaches by analyzing two human embryonic stem cell lines derived from genetically unrelated embryos and a matched pair of colon tumor and adjacent normal colon tissue obtained from the same donor. Our analysis reveals that methylated DNA immunoprecipitation sequencing (MeDIP-seq), methylated DNA capture by affinity purification (MethylCap-seq), reduced representation bisulfite sequencing (RRBS) and the Infinium HumanMethylation27 assay all produce accurate DNA methylation data. However, these methods differ in their ability to detect differentially methylated regions between pairs of samples. We highlight strengths and weaknesses of the four methods and give practical recommendations for the design of epigenomic case-control studies.

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Figure 1: Outline of the DNA methylation technology comparison.
Figure 2: Comparison of DNA methylation maps obtained with four different methods.
Figure 3: Quantification of DNA methylation with MeDIP-seq, MethylCap-seq and RRBS.
Figure 4: Genomic coverage of MeDIP-seq, MethylCap-seq, RRBS and Infinium.
Figure 5: Detection of DMRs with MeDIP-seq, MethylCap-seq and RRBS.

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Acknowledgements

We thank A. Crenshaw and M. Parkin (Broad Institute) for assistance with the Infinium assay and K. Halachev (Max Planck Institute for Informatics) for the provision of genome annotation files. C.B. is supported by a Feodor Lynen Fellowship from the Alexander von Humboldt Foundation. A.B.B. is supported by the Dutch Cancer Foundation (KWF, grant KUN 2008-4130). A.M. is supported by the Massachusetts Life Science Center and the Pew Charitable Trusts. The described work was in part funded by the Pew Charitable Trusts, the US National Institutes of Health Roadmap Initiative on Epigenomics (U01ES017155) and the European Union's CANCERDIP project (HEALTH-F2-2007-200620).

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Author notes

  1. Christoph Bock and Eleni M Tomazou: These authors contributed equally to this work.

Authors and Affiliations

  1. Broad Institute, Cambridge, Massachusetts, USA

    Christoph Bock, Eleni M Tomazou, Fabian Müller, Hongcang Gu, Natalie Jäger, Andreas Gnirke & Alexander Meissner

  2. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA

    Christoph Bock, Eleni M Tomazou, Fabian Müller, Natalie Jäger & Alexander Meissner

  3. Harvard Stem Cell Institute, Cambridge, Massachusetts, USA

    Christoph Bock, Eleni M Tomazou, Fabian Müller, Natalie Jäger & Alexander Meissner

  4. Max Planck Institute for Informatics, Saarbrücken, Germany

    Christoph Bock & Fabian Müller

  5. Radboud University Department of Molecular Biology, Nijmegen Center for Molecular Life Sciences, Nijmegen, The Netherlands

    Arie B Brinkman, Femke Simmer & Hendrik G Stunnenberg

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Contributions

C.B., E.M.T. and A.M. conceived and designed the study; E.M.T., A.B.B., F.S. and H.G. performed the experiments; C.B., F.M. and N.J. analyzed the data; C.B., A.G., H.G.S. and A.M. interpreted the results; and C.B. and A.M. wrote the paper.

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Correspondence to Christoph Bock or Alexander Meissner.

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Supplementary information

Supplementary Text and Figures

Supplementary Figs. 1–12 (PDF 2789 kb)

Supplementary Data 1

Validation of method-specific DMRs by clonal bisulfite sequencing (PDF 804 kb)

Supplementary Data 2

DNA methylation map of prototypic repeat sequences (PDF 4723 kb)

Supplementary Data 3

Differential DNA methylation of prototypic repeat sequences (PDF 3239 kb)

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Bock, C., Tomazou, E., Brinkman, A. et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 28, 1106–1114 (2010). https://doi.org/10.1038/nbt.1681

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