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.

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Abstract

We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Comparison of ChIP-Seq and ChIP-chip data.
Figure 2: Histone trimethylation state predicts expression of HCPs and LCPs.
Figure 3: Cell-type-specific chromatin marks at promoters.
Figure 4: Correlation between chromatin-state changes and lineage expression.
Figure 5: H3K4me3 and H3K36me3 annotate genes and non-coding RNA transcripts.
Figure 6: Allele-specific histone methylation and genic H3K9me3/H4K20me3.

References

  1. Surani, M. A., Hayashi, K. & Hajkova, P. Genetic and epigenetic regulators of pluripotency. Cell 128, 747–762 (2007)

    CAS  Article  Google Scholar 

  2. Bernstein, B. E., Meissner, A. & Lander, E. S. The mammalian epigenome. Cell 128, 669–681 (2007)

    CAS  Article  Google Scholar 

  3. Kouzarides, T. Chromatin modifications and their function. Cell 128, 693–705 (2007)

    CAS  Article  Google Scholar 

  4. Buck, M. J. & Lieb, J. D. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83, 349–360 (2004)

    CAS  Article  Google Scholar 

  5. Mockler, T. C. et al. Applications of DNA tiling arrays for whole-genome analysis. Genomics 85, 1–15 (2005)

    CAS  Article  Google Scholar 

  6. Roh, T. Y., Cuddapah, S. & Zhao, K. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev. 19, 542–552 (2005)

    CAS  Article  Google Scholar 

  7. Service, R. F. Gene sequencing. The race for the $1000 genome. Science 311, 1544–1546 (2006)

    CAS  Article  Google Scholar 

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

    Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  10. Ringrose, L. & Paro, R. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet. 38, 413–443 (2004)

    CAS  Article  Google Scholar 

  11. Schuettengruber, B., Chourrout, D., Vervoort, M., Leblanc, B. & Cavalli, G. Genome regulation by polycomb and trithorax proteins. Cell 128, 735–745 (2007)

    CAS  Article  Google Scholar 

  12. Azuara, V. et al. Chromatin signatures of pluripotent cell lines. Nature Cell Biol. 8, 532–538 (2006)

    CAS  Article  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)

    ADS  CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  16. Kim, T. H. et al. A high-resolution map of active promoters in the human genome. Nature 436, 876–880 (2005)

    ADS  CAS  Article  Google Scholar 

  17. Boyer, L. A. et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349–353 (2006)

    ADS  CAS  Article  Google Scholar 

  18. Lee, T. I. et al. Control of developmental regulators by polycomb in human embryonic stem cells. Cell 125, 301–313 (2006)

    CAS  Article  Google Scholar 

  19. Squazzo, S. L. et al. Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res. 16, 890–900 (2006)

    CAS  Article  Google Scholar 

  20. Pasini, D., Bracken, A. P., Hansen, J. B., Capillo, M. & Helin, K. The Polycomb Group protein Suz12 is required for Embryonic Stem Cell differentiation. Mol. Cell. Biol. 27, 3769–3779 (2007)

    CAS  Article  Google Scholar 

  21. Klose, R. J. & Bird, A. P. Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci. 31, 89–97 (2006)

    CAS  Article  Google Scholar 

  22. Wang, X., Su, H. & Bradley, A. Molecular mechanisms governing Pcdh-γ gene expression: evidence for a multiple promoter and cis-alternative splicing model. Genes Dev. 16, 1890–1905 (2002)

    CAS  Article  Google Scholar 

  23. Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559–1563 (2005)

    ADS  CAS  Article  Google Scholar 

  24. Alexander, D. L., Ganem, L. G., Fernandez-Salguero, P., Gonzalez, F. & Jefcoate, C. R. Aryl-hydrocarbon receptor is an inhibitory regulator of lipid synthesis and of commitment to adipogenesis. J. Cell Sci. 111, 3311–3322 (1998)

    CAS  PubMed  Google Scholar 

  25. Lengner, C. J. et al. Primary mouse embryonic fibroblasts: a model of mesenchymal cartilage formation. J. Cell. Physiol. 200, 327–333 (2004)

    CAS  Article  Google Scholar 

  26. Garreta, E., Genove, E., Borros, S. & Semino, C. E. Osteogenic differentiation of mouse embryonic stem cells and mouse embryonic fibroblasts in a three-dimensional self-assembling peptide scaffold. Tissue Eng. 12, 2215–2227 (2006)

    CAS  Article  Google Scholar 

  27. Doetsch, F. The glial identity of neural stem cells. Nature Neurosci. 6, 1127–1134 (2003)

    CAS  Article  Google Scholar 

  28. Krichevsky, A. M., Sonntag, K. C., Isacson, O. & Kosik, K. S. Specific microRNAs modulate embryonic stem cell-derived neurogenesis. Stem Cells 24, 857–864 (2006)

    CAS  Article  Google Scholar 

  29. Rao, B., Shibata, Y., Strahl, B. D. & Lieb, J. D. Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide. Mol. Cell. Biol. 25, 9447–9459 (2005)

    CAS  Article  Google Scholar 

  30. Bannister, A. J. et al. Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes. J. Biol. Chem. 280, 17732–17736 (2005)

    CAS  Article  Google Scholar 

  31. Kim, A., Kiefer, C. M. & Dean, A. Distinctive signatures of histone methylation in transcribed coding and noncoding human β-globin sequences. Mol. Cell. Biol. 27, 1271–1279 (2007)

    CAS  Article  Google Scholar 

  32. Vakoc, C. R., Sachdeva, M. M., Wang, H. & Blobel, G. A. Profile of histone lysine methylation across transcribed mammalian chromatin. Mol. Cell. Biol. 26, 9185–9195 (2006)

    CAS  Article  Google Scholar 

  33. Li, B., Carey, M. & Workman, J. L. The role of chromatin during transcription. Cell 128, 707–719 (2007)

    CAS  Article  Google Scholar 

  34. Fantes, J. et al. Mutations in SOX2 cause anophthalmia. Nature Genet. 33, 461–463 (2003)

    CAS  Article  Google Scholar 

  35. Hutchinson, J. N. et al. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 8, 39 (2007)

    Article  Google Scholar 

  36. Seitz, H. et al. A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. Genome Res. 14, 1741–1748 (2004)

    CAS  Article  Google Scholar 

  37. Cullen, B. R. Transcription and processing of human microRNA precursors. Mol. Cell 16, 861–865 (2004)

    CAS  Article  Google Scholar 

  38. Zaratiegui, M., Irvine, D. V. & Martienssen, R. A. Noncoding RNAs and gene silencing. Cell 128, 763–776 (2007)

    CAS  Article  Google Scholar 

  39. Verdel, A. & Moazed, D. RNAi-directed assembly of heterochromatin in fission yeast. FEBS Lett. 579, 5872–5878 (2005)

    CAS  Article  Google Scholar 

  40. Martens, J. H. et al. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J. 24, 800–812 (2005)

    CAS  Article  Google Scholar 

  41. Baust, C. et al. Structure and expression of mobile ETnII retroelements and their coding-competent MusD relatives in the mouse. J. Virol. 77, 11448–11458 (2003)

    CAS  Article  Google Scholar 

  42. Svoboda, P. et al. RNAi and expression of retrotransposons MuERV-L and IAP in preimplantation mouse embryos. Dev. Biol. 269, 276–285 (2004)

    CAS  Article  Google Scholar 

  43. Cho, D. H. et al. Antisense transcription and heterochromatin at the DM1 CTG repeats are constrained by CTCF. Mol. Cell 20, 483–489 (2005)

    CAS  Article  Google Scholar 

  44. Feng, Y. Q. et al. The human β-globin locus control region can silence as well as activate gene expression. Mol. Cell. Biol. 25, 3864–3874 (2005)

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  46. Delaval, K. et al. Differential histone modifications mark mouse imprinting control regions during spermatogenesis. EMBO J. 26, 720–729 (2007)

    CAS  Article  Google Scholar 

  47. Feil, R. & Berger, F. Convergent evolution of genomic imprinting in plants and mammals. Trends Genet. 23, 192–199 (2007)

    CAS  Article  Google Scholar 

  48. Strausberg, R. L. et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc. Natl Acad. Sci. USA 99, 16899–16903 (2002)

    ADS  Article  Google Scholar 

Download references

Acknowledgements

We thank S. Fisher, M. Kellis, B. Birren and M. Zody for technical assistance and constructive discussions. We acknowledge L. Zagachin in the MGH Nucleic Acid Quantitation core for assistance with real-time PCR. E.M. was supported by an institutional training grant from NIH. M.W. was supported by fellowships from the Human Frontiers Science Organization Program and the Ellison Foundation. This research was supported by funds from the National Human Genome Research Institute, the National Cancer Institute, the Burroughs Wellcome Fund, Massachusetts General Hospital, and the Broad Institute of MIT and Harvard.

All analysed data sets can be obtained from http://www.broad.mit.edu/seq_platform/chip/. Microarray data have been submitted to the GEO repository under accession number GSE8024.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Eric S. Lander or Bradley E. Bernstein.

Ethics declarations

Competing interests

Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Notes which includes the ChIP-Seq read requirement, genome coverage and accuracy and Supplementary Figures 1-10 with Legends (PDF 9260 kb)

Supplementary Table 1

This file contains Supplementary Table 1 which includes the list of datasets analyzed. (XLS 15 kb)

Supplementary Table 2

This file contains Supplementary Table 2 which includes the primers for RT-PCR validation of ChIP-Seq. (XLS 24 kb)

Supplementary Table 3

This file contains Supplementary Table 3 which includes the list of analyzed promoters and their chromatin state in ES cells, neural progenitors and embryonic fibroblasts. (XLS 3206 kb)

Supplementary Table 4

This file contains Supplementary Table 4 which includes the expression levels for analyzed genes in ES cells, neural progenitors and embryonic fibroblasts. (XLS 2070 kb)

Supplementary Table 5

This file contains Supplementary Table 5 which includes the Gene Ontology categories associated with monovalent and bivalent promoters in ES cells. (XLS 35 kb)

Supplementary Table 6

This file contains Supplementary Table 6 which includes the chromatin state of promoters associated with known regulators or markers of differentiated cell types (XLS 23 kb)

Supplementary Table 7

This file contains Supplementary Table 7 which includes the allelic bias observed at verified or putative imprinting control regions. (XLS 21 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Mikkelsen, T., Ku, M., Jaffe, D. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007). https://doi.org/10.1038/nature06008

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature06008

Further reading

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

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