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.
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Sasaki, H. & Matsui, Y. Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nature Rev. Genet. 2008, 129–140 (2008)
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)
Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935 (2009)
Blackledge, N. P. et al. CpG islands recruit a histone H3 lysine 36 demethylase. Mol. Cell 38, 179–190 (2010)
Thomson, J. P. et al. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464, 1082–1086 (2010)
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)
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)
Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genet. 39, 457–466 (2007)
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)
Ooi, S. K. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007)
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)
Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008)
Mikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007)
Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006)
Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009)
Boyer, L. A. et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349–353 (2006)
Lee, T. I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301–313 (2006)
Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043 (2002)
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)
Xiao, T. et al. Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev. 17, 654–663 (2003)
Ku, M. et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 4, e1000242 (2008)
Pasini, D. et al. JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells. Nature 464, 306–310 (2010)
Wu, H. et al. Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science 329, 444–448 (2010)
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)
Wu, S. C., Kallin, E. M. & Zhang, Y. Role of H3K27 methylation in the regulation of lncRNA expression. Cell Res. 20, 1109–1116 (2010)
Wang, Z. et al. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138, 1019–1031 (2009)
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008)
Seila, A. C. et al. Divergent transcription from active promoters. Science 322, 1849–1851 (2008)
Ji, H. et al. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nature Biotechnol. 26, 1293–1300 (2008)
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)
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.
The authors declare no competing financial interests.
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)
This table shows Tet1 binding sites in wild-type mouse ES cells. (XLS 3516 kb)
This table shows genomic regions associated with a significant increase in 5mC levels in response to Tet1-depletion. (XLS 5374 kb)
This table shows a summary of ChIP-Seq data used in data analysis. (XLS 11 kb)
This table shows chromatin states of Tet1 targets in mouse ES cells. (XLS 3287 kb)
This table shows differentially expressed genes between control and Tet1-depleted ES cells. (XLS 197 kb)
This table shows the effect of Nanog overexpression (OE) in Tet1 KD ES cells in dysregulated Tet1 direct targets. (XLS 104 kb)
This table shows genomic regions associated with a significant decrease in Ezh2 occupancy in response to Tet1-depletion. (XLS 4215 kb)
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) doi:10.1038/nature09934
Histone demethylase Kdm2a regulates germ cell genes and endogenous retroviruses in embryonic stem cells
Journal of Biological Chemistry (2019)
Epigenetics & Chromatin (2019)
New directions in treating peripheral T-cell lymphomas (PTCL): leveraging epigenetic modifiers alone and in combination
Expert Review of Hematology (2019)
Life Science Alliance (2019)