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Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

Nature Biotechnology volume 27, pages 361–368 (2009)Cite this article

A Corrigendum to this article was published on 01 May 2009

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Abstract

Studies of epigenetic modifications would benefit from improved methods for high-throughput methylation profiling. We introduce two complementary approaches that use next-generation sequencing technology to detect cytosine methylation. In the first method, we designed ∼10,000 bisulfite padlock probes to profile ∼7,000 CpG locations distributed over the ENCODE pilot project regions and applied them to human B-lymphocytes, fibroblasts and induced pluripotent stem cells. This unbiased choice of targets takes advantage of existing expression and chromatin immunoprecipitation data and enabled us to observe a pattern of low promoter methylation and high gene-body methylation in highly expressed genes. The second method, methyl-sensitive cut counting, generated nontargeted genome-scale data for ∼1.4 million HpaII sites in the DNA of B-lymphocytes and confirmed that gene-body methylation in highly expressed genes is a consistent phenomenon throughout the human genome. Our observations highlight the usefulness of techniques that are not inherently or intentionally biased towards particular subsets like CpG islands or promoter regions.

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Figure 1: BSPP technology enables accurate measurement of methylation levels.
Figure 2: Changes in methylation associated with position relative to genes differ between highly and weakly expressed genes.
Figure 3: MSCC technology enables accurate estimates of methylation.
Figure 4: The effects of promoter CpG density and methylation in genes with different levels of expression.
Figure 5: Methylation profiles of individual genes.

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Change history

  • 08 May 2009

    In the version of this article initially published, the second affilliation for Yuan Gao was omitted: Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia, USA. The affiliation has been added to the HTML and PDF versions of the article.

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Acknowledgements

We thank Kun Zhang for discussion throughout this work; Wei Lin for help with computational design; Andrew Chess and Ravid Straussman for discussion and critical reading of the manuscript; Harvard Biopolymers Facility for Solexa sequencing; and Harvard Partners Center for Genetics and Genomics for gene expression profiling. This work was supported by the NHGRI-Centers of Excellence in Genomic Science (to G.M.C.).

Author information

Author notes

  1. Madeleine P Ball and Jin Billy Li: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genetics, Harvard Medical School, Cambridge, Massachusetts, USA

    Madeleine P Ball, Jin Billy Li, Je-Hyuk Lee & George M Church

  2. Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA

    Madeleine P Ball, Jin Billy Li, Je-Hyuk Lee & George M Church

  3. Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA

    Yuan Gao & Bin Xie

  4. Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia, USA

    Yuan Gao

  5. Genomics Solution Unit, Agilent Technologies Inc., Santa Clara, California, USA

    Emily M LeProust

  6. Department of Medicine, Division of Pediatric Hematology Oncology, Children's Hospital Boston, and Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Karp Family Research Building 7214, Boston, Massachusetts, USA

    In-Hyun Park & George Q Daley

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Contributions

M.P.B., J.B.L. and G.M.C. conceived the study, designed the research and wrote the manuscript. M.P.B. and J.B.L. performed experiments and data analysis. Y.G. and B.X. carried out initial Solexa sequencing. J.-H.L. helped with culturing cell lines and isolating DNA/RNA. E.M.L. synthesized the padlock oligos. I.-H.P. and G.Q.D. generated the iPS cell lines.

Corresponding authors

Correspondence to Jin Billy Li or George M Church.

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Competing interests

E.M.L. is an employee of Agilent Technologies. G.M.C. is involved in eight next-generation sequencing companies. M.P.B., J.B.L. and G.M.C. are named as inventors on a patent application on technologies described in this article.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10; Supplementary Tables 2–5, 7,8 (PDF 6072 kb)

Supplementary Table 1

BSPP data (TXT 2113 kb)

Supplementary Table 6

MSCC data (TXT 60051 kb)

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Ball, M., Li, J., Gao, Y. et al. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27, 361–368 (2009). https://doi.org/10.1038/nbt.1533

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