Genome-scale DNA methylation maps of pluripotent and differentiated cells (original) (raw)

• Letter
• Published: 06 July 2008
• Tarjei S. Mikkelsen2,4 na1,
• Hongcang Gu2,
• Marius Wernig1,
• Jacob Hanna1,
• Andrey Sivachenko2,
• Xiaolan Zhang2,
• Bradley E. Bernstein2,5,6,
• Chad Nusbaum2,
• David B. Jaffe2,
• Andreas Gnirke2,
• Rudolf Jaenisch1,7 &
• …
• Eric S. Lander1,2,7,8

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

• 24k Accesses
• 1923 Citations
• 13 Altmetric
• Metrics details

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

Subscribe to this journal

Receive 51 print issues and online access

$199.00 per year

only $3.90 per issue

Buy this article

• Purchase on SpringerLink
• Instant access to full article PDF

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

Additional access options:

• Log in
• Learn about institutional subscriptions
• Read our FAQs
• Contact customer support

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
   You can also search for this author inPubMed Google Scholar
2. Tarjei S. Mikkelsen
   You can also search for this author inPubMed Google Scholar
3. Hongcang Gu
   You can also search for this author inPubMed Google Scholar
4. Marius Wernig
   You can also search for this author inPubMed Google Scholar
5. Jacob Hanna
   You can also search for this author inPubMed Google Scholar
6. Andrey Sivachenko
   You can also search for this author inPubMed Google Scholar
7. Xiaolan Zhang
   You can also search for this author inPubMed Google Scholar
8. Bradley E. Bernstein
   You can also search for this author inPubMed Google Scholar
9. Chad Nusbaum
   You can also search for this author inPubMed Google Scholar
10. David B. Jaffe
    You can also search for this author inPubMed Google Scholar
11. Andreas Gnirke
    You can also search for this author inPubMed Google Scholar
12. Rudolf Jaenisch
    You can also search for this author inPubMed Google Scholar
13. Eric S. Lander
    You can also search for this author inPubMed Google Scholar

Corresponding authors

Correspondence toRudolf 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

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: 24 March 2008
• Accepted: 21 May 2008
• Published: 06 July 2008
• Issue Date: 07 August 2008
• DOI: https://doi.org/10.1038/nature07107

This article is cited by

Editorial Summary

DNA methylation mapped

DNA methylation, an important mechanism of epigenetic modification that produces different patterns of gene expression from a single DNA sequence, is vital to normal development and its malfunction can cause cancer and other abnormalities. A map of DNA methylation in embryonic stem cells, and in various cell types derived from them, has now been produced at nucleotide resolution using high-throughput bisulphite sequencing combined with single molecule-based sequencing. The map reveals specific sites in the genome where methylation changes as cells develop, for instance when embryonic stem cells mature into nerve cells. More generally, the methodology will be of value for the epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.

Associated content