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Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome

Nature Genetics volume 39, pages 457466 (2007) | Download Citation

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Abstract

To gain insight into the function of DNA methylation at cis-regulatory regions and its impact on gene expression, we measured methylation, RNA polymerase occupancy and histone modifications at 16,000 promoters in primary human somatic and germline cells. We find CpG-poor promoters hypermethylated in somatic cells, which does not preclude their activity. This methylation is present in male gametes and results in evolutionary loss of CpG dinucleotides, as measured by divergence between humans and primates. In contrast, strong CpG island promoters are mostly unmethylated, even when inactive. Weak CpG island promoters are distinct, as they are preferential targets for de novo methylation in somatic cells. Notably, most germline-specific genes are methylated in somatic cells, suggesting additional functional selection. These results show that promoter sequence and gene function are major predictors of promoter methylation states. Moreover, we observe that inactive unmethylated CpG island promoters show elevated levels of dimethylation of Lys4 of histone H3, suggesting that this chromatin mark may protect DNA from methylation.

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Acknowledgements

We thank members of the Schübeler laboratory for advice during the course of the project and comments on the manuscript; E. Oakeley for generating scripts for data reformatting, A. Peters, M. Lorincz, C. Alvarez, P. de Boer, E. Selker and M. Groudine for critical reading of the manuscript. Primary samples from kidney and colon were obtained from M. Haase (Dresden University of Technology). Work in the laboratory of D.S. is supported by the Novartis Research Foundation, the EU 6th framework program NOE 'The Epigenome' (LSHG-CT-2004-503433) and a European Molecular Biology Organization (EMBO) Young Investigator Award. I.H. is supported by an EMBO long-term fellowship (ALTF 1160-2005).

Author information

Affiliations

  1. Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.

    • Michael Weber
    • , Michael B Stadler
    • , Michael Rebhan
    •  & Dirk Schübeler
  2. Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany.

    • Ines Hellmann
    •  & Svante Pääbo
  3. University of Copenhagen, Universitetsparken 15, Copenhagen , Denmark, 2100.

    • Ines Hellmann
  4. Department of Obstetrics and Gynaecology, Radboud University Nijmegen Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.

    • Liliana Ramos

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Contributions

M.W. designed and performed experiments and analysis and wrote the manuscript. D.S. designed the study and wrote the manuscript. M.B.S. performed housekeeping annotations and wrote custom software. M.R. performed CpG classifications and promoter confidence analysis, retrieved genomic information and contributed to the writing of the manuscript. I.H. and S.P. performed divergence analysis and contributed to the writing of the manuscript. L.R. provided purified human samples.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Dirk Schübeler.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    Validation of the spatial filtering of oligos.

  2. 2.

    Supplementary Fig. 2

    Reproducibility of microarray experiments.

  3. 3.

    Supplementary Fig. 3

    Higher promoter methylation on the X chromosome compared with autosomes.

  4. 4.

    Supplementary Fig. 4

    Bisulfite genomic sequencing of CpG island promoters.

  5. 5.

    Supplementary Fig. 5

    DNA methylation of active LCP promoters.

  6. 6.

    Supplementary Fig. 6

    Comparison of promoter DNA methylation patterns between sperm and primary fibroblasts.

  7. 7.

    Supplementary Table 1

    Promoter DNA methylation of germline-specific genes in primary fibroblasts and sperm.

  8. 8.

    Supplementary Table 2

    Primer sequences.

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DOI

https://doi.org/10.1038/ng1990

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