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

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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.

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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.

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Primary accessions

Gene Expression Omnibus

Data deposits

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

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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

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.

Correspondence to Yi Zhang.

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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)

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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) doi:10.1038/nature09934

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