TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity (original) (raw)

Nature volume 473, pages 343–348 (2011)Cite this article

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Abstract

Enzymes catalysing the methylation of the 5-position of cytosine (mC) have essential roles in regulating gene expression and maintaining cellular identity. Recently, TET1 was found to hydroxylate the methyl group of mC, converting it to 5-hydroxymethyl cytosine (hmC). Here we show that TET1 binds throughout the genome of embryonic stem cells, with the majority of binding sites located at transcription start sites (TSSs) of CpG-rich promoters and within genes. The hmC modification is found in gene bodies and in contrast to mC is also enriched at CpG-rich TSSs. We provide evidence further that TET1 has a role in transcriptional repression. TET1 binds a significant proportion of Polycomb group target genes. Furthermore, TET1 associates and colocalizes with the SIN3A co-repressor complex. We propose that TET1 fine-tunes transcription, opposes aberrant DNA methylation at CpG-rich sequences and thereby contributes to the regulation of DNA methylation fidelity.

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Gene Expression Omnibus

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ChIP-seq and gene expression data are available at the Gene Expression Omnibus (GEO) under accession GSE24843.

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Acknowledgements

We thank U. Toftegaard for excellent technical help, M. Okano for the donation of TKO ES cells, and members of the Helin lab for discussions. M.T.P. was supported by a fellowship from the Danish Cancer Society. J.R. is a senior research fellow of the Wellcome Trust. The work in the Helin lab was supported by grants from the Excellence Program of the University of Copenhagen, the Danish National Research Foundation, the Danish Cancer Society, the Lundbeck foundation, the Novo Nordisk Foundation, and the Danish Medical Research Council.

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Author notes

  1. Kristine Williams, Jesper Christensen and Marianne Terndrup Pedersen: These authors contributed equally to this work.

Authors and Affiliations

  1. Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
    Kristine Williams, Jesper Christensen, Marianne Terndrup Pedersen, Jens V. Johansen, Paul A. C. Cloos & Kristian Helin
  2. Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
    Kristine Williams, Jesper Christensen, Marianne Terndrup Pedersen, Paul A. C. Cloos & Kristian Helin
  3. Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
    Jens V. Johansen
  4. Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
    Juri Rappsilber

Authors

  1. Kristine Williams
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  2. Jesper Christensen
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  3. Marianne Terndrup Pedersen
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  4. Jens V. Johansen
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  5. Paul A. C. Cloos
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  6. Juri Rappsilber
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  7. Kristian Helin
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Contributions

K.W. performed the major part of experiments in Figs 1, 3, 4a, b, h and Supplementary Figs 1a–c, 2, 3, 5, 7a, 9a–d, 10a, 11 and 12c, d. J.C. developed and characterized the new reagents used in this study, and participated in most experiments. M.T.P. performed the major part of experiments in Figs 2, 4c, g and Supplementary Figs 1d, 6b, 7b, c, 8, 10b and 12a, b. J.V.J. performed bioinformatics analyses. P.A.C.C. assisted in characterizing reagents. J.R performed the mass spectrometry analysis. J.C. and K.H. supervised the project and all authors contributed to the writing of the manuscript.

Corresponding author

Correspondence toKristian Helin.

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Competing interests

K.H., J.C. and P.A.C.C. are cofounders of EpiTherapeutics and have shares and warrants in the company. All other authors declare that they have no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-12 with legends and additional references. (PDF 615 kb)

Supplementary Table 1

This table shows ChIP-seq identified target genes for Tet1-N, Tet1-C, Sin3A (Abcam), Sin3A (S.Cruz). (XLS 541 kb)

Supplementary Table 2

This table shows hmC status of genes reported to become DNA methylated during differentiation. (XLS 82 kb)

Supplementary Table 3

This table shows Tet1 knockdown microarray data. (XLS 10245 kb)

Supplementary Table 4

This table shows Sin3A knockdown microarray data. (XLS 7690 kb)

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Williams, K., Christensen, J., Pedersen, M. et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity.Nature 473, 343–348 (2011). https://doi.org/10.1038/nature10066

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Editorial Summary

Fine-tuning DNA methylation by Tet proteins

The modified DNA base 5-hydroxymethylcytosine (5hmC), sometimes called the sixth base, is present in the mammalian genome where it is generated by oxidation of 5-methylcytosine (5mC; the fifth base) by enzymes of the Tet family. Four papers in this issue, from the Helin, Zhang, Rao and Reik laboratories, respectively, report on the genome-wide distribution of Tet1 and/or 5hmC in mouse embryonic stem cells using the ChIP-seq technique. Links between Tet1 and transcription regulation — both activation and repression — are revealed. Anjana Rao and colleagues also describe two alternative methods with increased sensitivity for mapping single 5hmC bases. In the associated News & Views, Nathalie Véron and Antoine H. F. M. Peters discuss what these and other recent papers reveal about the role of Tet proteins in regulating DNA methylation and gene expression.

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