Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Genome-scale DNA methylation maps of pluripotent and differentiated cells

Nature volume 454, pages 766–770 (2008)Cite this article

Abstract

DNA methylation is essential for normal development1,2,3 and has been implicated in many pathologies including cancer4,5. Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone methylation and other chromatin modifications in mammals remains limited. Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput reduced representation bisulphite sequencing6 and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of embryonic-stem-cell-derived and primary cells reveals that ‘weak’ CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumours. More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: CpG methylation levels in ES cells and NPCs for CpGs with ≥10-fold coverage.
Figure 2: Correlation between DNA and histone methylation.
Figure 3: Developmentally regulated de-methylation of highly conserved non-coding elements.
Figure 4: HCP hypermethylation of cultured cells.

Similar content being viewed by others

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

All primary sequencing data have been submitted to the NCBI GEO repository under accession numbers GSE11034 (RRBS), GSE11172 (ChIP-Seq) and GSE11483 (gene expression microarrays).

References

  1. Bestor, T. H. The DNA methyltransferases of mammals. Hum. Mol. Genet. 9, 2395–2402 (2000)

    Article  CAS  Google Scholar 

  2. Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002)

    Article  CAS  Google Scholar 

  3. Reik, W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447, 425–432 (2007)

    Article  ADS  CAS  Google Scholar 

  4. Feinberg, A. P. The epigenetics of cancer etiology. Semin. Cancer Biol. 14, 427–432 (2004)

    Article  CAS  Google Scholar 

  5. Jones, P. A. & Baylin, S. B. The epigenomics of cancer. Cell 128, 683–692 (2007)

    Article  CAS  Google Scholar 

  6. Meissner, A. et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 33, 5868–5877 (2005)

    Article  CAS  Google Scholar 

  7. Frommer, M. et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl Acad. Sci. USA 89, 1827–1831 (1992)

    Article  ADS  CAS  Google Scholar 

  8. Eckhardt, F. et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nature Genet. 38, 1378–1385 (2006)

    Article  CAS  Google Scholar 

  9. Cokus, S. J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008)

    Article  ADS  CAS  Google Scholar 

  10. Altshuler, D. et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513–516 (2000)

    Article  ADS  CAS  Google Scholar 

  11. Mikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007)

    Article  ADS  CAS  Google Scholar 

  12. Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genet. 39, 457–466 (2007)

    Article  CAS  Google Scholar 

  13. Saxonov, S., Berg, P. & Brutlag, D. L. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl Acad. Sci. USA 103, 1412–1417 (2006)

    Article  ADS  CAS  Google Scholar 

  14. Bernstein, B. et al. A bivalent chromatin structure marks key Developmental genes in embryonic stem cells. Cell 125, 315–326 (2006)

    Article  CAS  Google Scholar 

  15. Illingworth, R. et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 6, e22 (2008)

    Article  Google Scholar 

  16. West, A. G. & Fraser, P. Remote control of gene transcription. Hum. Mol. Genet. 14 (Spec No 1) R101–R111 (2005)

    Article  CAS  Google Scholar 

  17. Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genet. 39, 311–318 (2007)

    Article  CAS  Google Scholar 

  18. Bernstein, B. E. et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169–181 (2005)

    Article  CAS  Google Scholar 

  19. Edwards, C. A. & Ferguson-Smith, A. C. Mechanisms regulating imprinted genes in clusters. Curr. Opin. Cell Biol. 19, 281–289 (2007)

    Article  CAS  Google Scholar 

  20. Ooi, S. K. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007)

    Article  ADS  CAS  Google Scholar 

  21. Esteve, P. O. et al. Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication. Genes Dev. 20, 3089–3103 (2006)

    Article  CAS  Google Scholar 

  22. Conti, L. et al. Niche-independent symmetrical self-renewal of a mammalian tissue stem cell. PLoS Biol. 3, e283 (2005)

    Article  Google Scholar 

  23. Voo, K. S., Carlone, D. L., Jacobsen, B. M., Flodin, A. & Skalnik, D. G. Cloning of a mammalian transcriptional activator that binds unmethylated CpG motifs and shares a CXXC domain with DNA methyltransferase, human trithorax, and methyl-CpG binding domain protein 1. Mol. Cell. Biol. 20, 2108–2121 (2000)

    Article  CAS  Google Scholar 

  24. Sharma, M. K. et al. Distinct genetic signatures among pilocytic astrocytomas relate to their brain region origin. Cancer Res. 67, 890–900 (2007)

    Article  CAS  Google Scholar 

  25. Aubert, J. et al. Screening for mammalian neural genes via fluorescence-activated cell sorter purification of neural precursors from Sox1–gfp knock-in mice. Proc. Natl Acad. Sci. USA 100 (Suppl 1). 11836–11841 (2003)

    Article  ADS  CAS  Google Scholar 

  26. Jones, P. A., Wolkowicz, M. J., Harrington, M. A. & Gonzales, F. Methylation and expression of the Myo D1 determination gene. Phil. Trans. R. Soc. Lond. B 326, 277–284 (1990)

    Article  ADS  CAS  Google Scholar 

  27. Smiraglia, D. J. et al. Excessive CpG island hypermethylation in cancer cell lines versus primary human malignancies. Hum. Mol. Genet. 10, 1413–1419 (2001)

    Article  CAS  Google Scholar 

  28. Shen, Y., Chow, J., Wang, Z. & Fan, G. Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells. Hum. Mol. Genet. 15, 2623–2635 (2006)

    Article  CAS  Google Scholar 

  29. Bouhon, I. A., Joannides, A., Kato, H., Chandran, S. & Allen, N. D. Embryonic stem cell-derived neural progenitors display temporal restriction to neural patterning. Stem Cells 24, 1908–1913 (2006)

    Article  CAS  Google Scholar 

  30. Ohm, J. E. & Baylin, S. B. Stem cell chromatin patterns: an instructive mechanism for DNA hypermethylation? Cell Cycle 6, 1040–1043 (2007)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank the staff of the Broad Institute Genome Sequencing Platform for assistance with data generation and B. Ramsahoye for the nearest neighbour analysis. This research was supported by funds from the National Human Genome Research Institute, the National Cancer Institute, and the Broad Institute of MIT and Harvard.

Author information

Author notes

  1. Alexander Meissner and Tarjei S. Mikkelsen: These authors contributed equally to this work.

Authors and Affiliations

  1. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA ,

    Alexander Meissner, Marius Wernig, Jacob Hanna, Rudolf Jaenisch & Eric S. Lander

  2. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA ,

    Alexander Meissner, Tarjei S. Mikkelsen, Hongcang Gu, Andrey Sivachenko, Xiaolan Zhang, Bradley E. Bernstein, Chad Nusbaum, David B. Jaffe, Andreas Gnirke & Eric S. Lander

  3. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA,

    Alexander Meissner

  4. Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA,

    Tarjei S. Mikkelsen

  5. Molecular Pathology Unit and Center for Cancer Research, MGH, Charlestown, Massachusetts 02129, USA ,

    Bradley E. Bernstein

  6. Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA,

    Bradley E. Bernstein

  7. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA,

    Rudolf Jaenisch & Eric S. Lander

  8. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02114, USA,

    Eric S. Lander

Authors
  1. Alexander Meissner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tarjei S. Mikkelsen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hongcang Gu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Marius Wernig
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jacob Hanna
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Andrey Sivachenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Xiaolan Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Bradley E. Bernstein
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Chad Nusbaum
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. David B. Jaffe
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Andreas Gnirke
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Rudolf Jaenisch
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Eric S. Lander
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Rudolf Jaenisch or Eric S. Lander.

Supplementary information

Supplementary Information 1

This file contains Supplementary Tables S1-S7 and Supplementary Figures S1-S9 with Legends. (PDF 11442 kb)

Supplementary Information 2

The file contains Supplementary Data S1. DNA and histone methylation states, and associated expression levels, for all analyzed high-CpG density promoters. (XLS 5606 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Meissner, A., Mikkelsen, T., Gu, H. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008). https://doi.org/10.1038/nature07107

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature07107

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing