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.

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells

Nature volume 473, pages 389–393 (2011)Cite this article

Subjects

Abstract

Epigenetic modification of the mammalian genome by DNA methylation (5-methylcytosine) has a profound impact on chromatin structure, gene expression and maintenance of cellular identity1. The recent demonstration that members of the Ten-eleven translocation (Tet) family of proteins can convert 5-methylcytosine to 5-hydroxymethylcytosine raised the possibility that Tet proteins are capable of establishing a distinct epigenetic state2,3. We have recently demonstrated that Tet1 is specifically expressed in murine embryonic stem (ES) cells and is required for ES cell maintenance2. Using chromatin immunoprecipitation coupled with high-throughput DNA sequencing, here we show in mouse ES cells that Tet1 is preferentially bound to CpG-rich sequences at promoters of both transcriptionally active and Polycomb-repressed genes. Despite an increase in levels of DNA methylation at many Tet1-binding sites, Tet1 depletion does not lead to downregulation of all the Tet1 targets. Interestingly, although Tet1-mediated promoter hypomethylation is required for maintaining the expression of a group of transcriptionally active genes, it is also involved in repression of Polycomb-targeted developmental regulators. Tet1 contributes to silencing of this group of genes by facilitating recruitment of PRC2 to CpG-rich gene promoters. Thus, our study not only establishes a role for Tet1 in modulating DNA methylation levels at CpG-rich promoters, but also reveals a dual function of Tet1 in promoting transcription of pluripotency factors as well as participating in the repression of Polycomb-targeted developmental regulators.

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

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

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

Figure 1: Tet1 is enriched at genomic regions with high-density CpG dinucleotides.
Figure 2: Tet1 maintains a DNA hypomethylated state at Tet1-bound regions.
Figure 3: Tet1 binds to and functions in both repressed (bivalent) and actively transcribed (H3K4me3-only) genes.
Figure 4: Tet1 is required for chromatin binding of PRC2 in mouse ES cells.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

ChIP-seq and microarray data have been deposited in the Gene Expression Omnibus under accession number GSE26833.

References

  1. Sasaki, H. & Matsui, Y. Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nature Rev. Genet. 2008, 129–140 (2008)

    Article  CAS  Google Scholar 

  2. Ito, S. et al. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466, 1129–1133 (2010)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  3. Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935 (2009)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  4. Blackledge, N. P. et al. CpG islands recruit a histone H3 lysine 36 demethylase. Mol. Cell 38, 179–190 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Thomson, J. P. et al. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464, 1082–1086 (2010)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  6. Liu, X. S., Brutlag, D. L. & Liu, J. S. An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nature Biotechnol. 20, 835–839 (2002)

    Article  CAS  Google Scholar 

  7. Fouse, S. D. et al. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell 2, 160–169 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. 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  PubMed  Google Scholar 

  9. Mohn, F. et al. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol. Cell 30, 755–766 (2008)

    Article  CAS  PubMed  Google Scholar 

  10. 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  PubMed  PubMed Central  Google Scholar 

  11. Schlesinger, Y. et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nature Genet. 39, 232–236 (2007)

    Article  CAS  PubMed  Google Scholar 

  12. Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  13. 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  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  15. Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  ADS  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043 (2002)

    Article  ADS  CAS  PubMed  Google Scholar 

  19. Kuzmichev, A., Nishioka, K., Erdjument-Bromage, H., Tempst, P. & Reinberg, D. Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16, 2893–2905 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Xiao, T. et al. Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev. 17, 654–663 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Ku, M. et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 4, e1000242 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Pasini, D. et al. JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells. Nature 464, 306–310 (2010)

    Article  ADS  CAS  PubMed  Google Scholar 

  23. Wu, H. et al. Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science 329, 444–448 (2010)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  24. Koh, K. P. et al. Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 8, 200–213 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Wu, S. C., Kallin, E. M. & Zhang, Y. Role of H3K27 methylation in the regulation of lncRNA expression. Cell Res. 20, 1109–1116 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Wang, Z. et al. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138, 1019–1031 (2009)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Seila, A. C. et al. Divergent transcription from active promoters. Science 322, 1849–1851 (2008)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  29. Ji, H. et al. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nature Biotechnol. 26, 1293–1300 (2008)

    Article  CAS  Google Scholar 

  30. Pelizzola, M. et al. MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Genome Res. 18, 1652–1659 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank B. Abraham and I. Chepelev for Illumina sequencing and data transfer; J. He and A. T. Nguyen for FACS sorting; O. Taranova for discussion; S. Wu for critical reading of the manuscript. This work was supported by NIH grants GM68804 (to Y.Z.), R56MH082068 (to Y.E.S.) and support from the Division of Intramural Research Program of National Heart, Lung and Blood Institute, NIH (K.Z.). S.I. is a research fellow of the Japan Society for the Promotion of Science. Y.Z. is an Investigator of the Howard Hughes Medical Institute.

Author information

Author notes

  1. Hao Wu

    Present address: Present address: Cardiovascular Research Centre, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA and Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA.,

  2. Hao Wu and Ana C. D’Alessio: These authors contributed equally to this work.

Authors and Affiliations

  1. Departments of Molecular & Medical Pharmacology and Psychiatry & Biobehavioral Sciences, IDDRC at Semel Institute of Neuroscience and Human Behavior, UCLA David Geffen School of Medicine, Los Angeles, 90095, California, USA

    Hao Wu & Yi Eve Sun

  2. Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, 27599-7295, North Carolina, USA

    Ana C. D’Alessio, Shinsuke Ito, Kai Xia & Yi Zhang

  3. Department of Environmental Health Sciences, Laboratory of Human Environmental Epigenomes, Johns Hopkins Bloomberg School of Public Health, Baltimore, 21025, Maryland, USA

    Zhibin Wang

  4. Laboratory of Molecular Immunology, The National Heart, Lung, and Blood Institute, NIH, Bethesda, 20892, Maryland, USA

    Kairong Cui & Keji Zhao

Authors
  1. Hao Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ana C. D’Alessio
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Shinsuke Ito
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kai Xia
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zhibin Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Kairong Cui
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Keji Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yi Eve Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Yi Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Y.Z. conceived the project; H.W., A.C.D’A. and Y.Z. designed the experiments; H.W., A.C.D’A., S.I., Z.W. and K.C. performed the experiments; H.W. and K.X. analysed the data; H.W., A.C.D’A., K.Z., Y.E.S. and Y.Z. interpreted the data; H.W. and Y.Z. wrote the manuscript.

Corresponding author

Correspondence to Yi Zhang.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains a Supplementary Discussion, additional references, Supplementary Figures 1-12 with legends and Supplementary Tables 8-10 (see separate files for Supplementary Tables 1-7). (PDF 6508 kb)

Supplementary Table 1

This table shows Tet1 binding sites in wild-type mouse ES cells. (XLS 3516 kb)

Supplementary Table 2

This table shows genomic regions associated with a significant increase in 5mC levels in response to Tet1-depletion. (XLS 5374 kb)

Supplementary Table 3

This table shows a summary of ChIP-Seq data used in data analysis. (XLS 11 kb)

Supplementary Table 4

This table shows chromatin states of Tet1 targets in mouse ES cells. (XLS 3287 kb)

Supplementary Table 5

This table shows differentially expressed genes between control and Tet1-depleted ES cells. (XLS 197 kb)

Supplementary Table 6

This table shows the effect of Nanog overexpression (OE) in Tet1 KD ES cells in dysregulated Tet1 direct targets. (XLS 104 kb)

Supplementary Table 7

This table shows genomic regions associated with a significant decrease in Ezh2 occupancy in response to Tet1-depletion. (XLS 4215 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Wu, H., D’Alessio, A., Ito, S. et al. Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 473, 389–393 (2011). https://doi.org/10.1038/nature09934

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature09934

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