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

Nature Genetics volume 39, pages 457–466 (2007)Cite this article

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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Figure 1: Defining the promoter methylome in human primary fibroblasts.
Figure 2: Promoter classification based on CpG representation.
Figure 3: Frequency of DNA methylation in promoter classes.
Figure 4: Functional consequence of DNA methylation on promoter activity depends on CpG content.
Figure 5: Elevated levels of H3K4 dimethylation mark inactive CpG islands.
Figure 6: Promoter DNA methylation in the germline is associated with CpG loss.
Figure 7: Methylation of promoters associated with germline-specific genes in somatic cells.
Figure 8: Regulation of promoter DNA methylation in the human genome.

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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

Authors and Affiliations

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

    Michael Weber, Michael B Stadler, Michael Rebhan & Dirk Schübeler

  2. Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D-04103, Germany

    Ines Hellmann & Svante Pääbo

  3. University of Copenhagen, Universitetsparken 15, Copenhagen ∅, 2100, Denmark

    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.

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Correspondence to Dirk Schübeler.

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Supplementary information

Supplementary Fig. 1

Validation of the spatial filtering of oligos. (PDF 202 kb)

Supplementary Fig. 2

Reproducibility of microarray experiments. (PDF 160 kb)

Supplementary Fig. 3

Higher promoter methylation on the X chromosome compared with autosomes. (PDF 106 kb)

Supplementary Fig. 4

Bisulfite genomic sequencing of CpG island promoters. (PDF 199 kb)

Supplementary Fig. 5

DNA methylation of active LCP promoters. (PDF 184 kb)

Supplementary Fig. 6

Comparison of promoter DNA methylation patterns between sperm and primary fibroblasts. (PDF 162 kb)

Supplementary Table 1

Promoter DNA methylation of germline-specific genes in primary fibroblasts and sperm. (PDF 52 kb)

Supplementary Table 2

Primer sequences. (PDF 54 kb)

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Weber, M., Hellmann, I., Stadler, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39, 457–466 (2007). https://doi.org/10.1038/ng1990

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