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TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

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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Figure 1: Identification of TET1 target genes.
Figure 2: Hydroxymethylcytosine localizes to TSS and gene body.
Figure 3: Knockdown of Tet1 in ES cells affects transcription.
Figure 4: TET1 interacts with SIN3A.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

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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Authors

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 to Kristian Helin.

Ethics declarations

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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