TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity
Open accessAbstract
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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Twenty-two differentially expressed E3 ligase genes may be epigenetically regulated by Tet1.
“identifying 22 differentially expressed E3 ligase genes that may undergo epigenetic regulation by Tet1 (supplemental Table 1).”
From RNF217 regulates iron homeostasis through its E3 ubiquitin ligase activity by modulating ferroportin degradation (2021) · cites this paper as [47]
HDAC1/2 themselves and their related complex components Sin3A and LSD1 all map within the vicinity of transcriptional start sites.
“This is perhaps unsurprising since HDAC1/2 themselves (Fig. 4C) and their related complex components, Sin3A37 and LSD138, all map within the vicinity of TSS.”
From Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo (2018) · cites this paper as [37]
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Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1
Tahiliani, M., Koh, K. P., Shen, Y., Pastor, W. A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L. M., Liu, D. R., Aravind, L., et al. (2009) · Science · doi:10.1126/science.1170116 · Cited by 5,836 · see citing works
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129 · see citing works
DNA methylation landscapes: Provocative insights from epigenomics
Suzuki, M. M., & Bird, A. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2341 · Cited by 3,039 · see citing works
The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain
Kriaucionis, S., & Heintz, N. (2009) · Science · doi:10.1126/science.1169786 · Cited by 2,700 · see citing works
Ito, S., D’Alessio, A. C., Taranova, O., Hong, K., Sowers, L. C., & Zhang, Y. (2010) · Nature · doi:10.1038/nature09303 · Cited by 2,542 · see citing works
Genome-scale DNA methylation maps of pluripotent and differentiated cells
Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B., et al. (2008) · Nature · doi:10.1038/nature07107 · Cited by 2,536 · see citing works
Linking DNA methylation and histone modification: patterns and paradigms
Cedar, H., & Bergman, Y. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2540 · Cited by 2,267 · see citing works
Weber, M., Davies, J. J., Wittig, D., Oakeley, E., Haase, M., Lam, W., & Schübeler, D. (2005) · Nature Genetics · doi:10.1038/ng1598 · Cited by 1,885 · see citing works
Mutation in <i>TET2</i> in Myeloid Cancers
Delhommeau, F., Dupont, S., Valle, V. D., James, C., Trannoy, S., Massé, A., Kosmider, O., Le Couedic, J.-P., Robert, F., Alberdi, A., et al. (2009) · New England Journal of Medicine · doi:10.1056/nejmoa0810069 · Cited by 1,776 · see citing works
Conserved role of intragenic DNA methylation in regulating alternative promoters
Maunakea, A. K., Nagarajan, R. P., Bilenky, M., Ballinger, T. J., D’Souza, C., Fouse, S. D., Johnson, B. E., Hong, C., Nielsen, C., Zhao, Y., et al. (2010) · Nature · doi:10.1038/nature09165 · Cited by 1,743 · see citing works
Comprehensive analysis of CpG islands in human chromosomes 21 and 22
Takai, D., & Jones, P. A. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052410099 · Cited by 1,507 · see citing works
Saxonov, S., Berg, P., & Brutlag, D. L. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510310103 · Cited by 1,401 · see citing works
Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells
Marson, A., Levine, S. S., Cole, M. F., Frampton, G. M., Brambrink, T., Johnstone, S. E., Guenther, M. G., Johnston, W. K., Wernig, M., Newman, J. J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.07.020 · Cited by 1,361 · see citing works
c-Myc Regulates Transcriptional Pause Release
Rahl, P. B., Lin, C. Y., Seila, A. C., Flynn, R. A., McCuine, S., Burge, C. B., Sharp, P. A., & Young, R. A. (2010) · Cell · doi:10.1016/j.cell.2010.03.030 · Cited by 1,279 · see citing works
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine
Song, C., Szulwach, K. E., Fu, Y., Dai, Q., Yi, C., Li, X., Li, Y., Chen, C.-H., Zhang, W., Jian, X., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1732 · Cited by 1,089 · see citing works
Mohn, F., Weber, M., Rebhan, M., Roloff, T. C., Richter, J., Stadler, M. B., Bibel, M., & Schübeler, D. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.05.007 · Cited by 912 · see citing works
Koh, K. P., Yabuuchi, A., Rao, S., Huang, Y., Cunniff, K., Nardone, J., Laiho, A., Tahiliani, M., Sommer, C. A., Mostoslavsky, G., et al. (2011) · Cell Stem Cell · doi:10.1016/j.stem.2011.01.008 · Cited by 776 · see citing works
An integrated software system for analyzing ChIP-chip and ChIP-seq data
Ji, H., Jiang, H., Ma, W., Johnson, D. S., Myers, R., & Wong, W. H. (2008) · Nature Biotechnology · doi:10.1038/nbt.1505 · Cited by 716 · see citing works
The Polycomb Group Protein Suz12 Is Required for Embryonic Stem Cell Differentiation
Pasini, D., Bracken, A. P., Hansen, J. B., Capillo, M., & Helin, K. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01432-06 · Cited by 696 · see citing works
Self-citationThe UCSC Genome Browser database: update 2010
Rhead, B. L., Karolchik, D., Kuhn, R. M., Hinrichs, A. S., Zweig, A. S., Fujita, P. A., Diekhans, M., Smith, K. E., Rosenbloom, K. R., Raney, B. J., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp939 · Cited by 567 · see citing works
JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells
Pasini, D., Cloos, P. A., Walfridsson, J., Olsson, L., Bukowski, J., Johansen, J. V., Bak, M., Tommerup, N., Rappsilber, J., & Helin, K. (2010) · Nature · doi:10.1038/nature08788 · Cited by 562 · see citing works
Self-citationTsumura, A., Hayakawa, T., Kumaki, Y., Takebayashi, S., Sakaue, M., Matsuoka, C., Shimotohno, K., Ishikawa, F., Li, E., Ueda, H. R., et al. (2006) · Genes to Cells · doi:10.1111/j.1365-2443.2006.00984.x · Cited by 544 · see citing works
Fouse, S. D., Shen, Y., Pellegrini, M. A., Cole, S. W., Meissner, A., Neste, L. V., Jaenisch, R., & Fan, G. (2008) · Cell stem cell · doi:10.1016/j.stem.2007.12.011 · Cited by 452 · see citing works
ANTIBODIES SPECIFIC FOR RIBONUCLEOSIDES AND RIBONUCLEOTIDES AND THEIR REACTION WITH DNA
Erlanger, B. F., & Beiser, S. M. (1964) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.52.1.68 · Cited by 449 · see citing works
Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA
Szwagierczak, A., Bultmann, S., Schmidt, C. S., Spada, F., & Leonhardt, H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq684 · Cited by 433 · see citing works
Cancer Epigenetics: Modifications, Screening, and Therapy
Gal‐Yam, E. N., Saito, Y., Egger, G., & Jones, P. A. (2007) · Annual Review of Medicine · doi:10.1146/annurev.med.59.061606.095816 · Cited by 269 · see citing works
Sin3: Master scaffold and transcriptional corepressor
Grzenda, A. L., Lomberk, G. A., Zhang, J., & Urrutia, R. A. (2009) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2009.05.007 · Cited by 241 · see citing works
Chávez, L., Józefczuk, J., Grimm, C., Dietrich, J., Timmermann, B., Lehrach, H. R., Herwig, R., & Adjaye, J. (2010) · Genome Research · doi:10.1101/gr.110114.110 · Cited by 176 · see citing works
Novel TET2 Mutations Associated With UPD4q24 in Myelodysplastic Syndrome
Mohamedali, A. M., Smith, A., Gäken, J. A., Lea, N. C., Mian, S. A., Westwood, N., Strupp, C., Gattermann, N., Germing, U., & Mufti, G. J. (2009) · Journal of Clinical Oncology · doi:10.1200/jco.2009.22.6985 · Cited by 83 · see citing works
Flagged first, then by citations
1 of the 30 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Functions of DNA methylation: islands, start sites, gene bodies and beyond
Jones, P. A. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3230 · Cited by 6,061 · see citing works
DNA methylation: roles in mammalian development
Smith, Z. D., & Meissner, A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3354 · Cited by 3,045 · see citing works
A decade of exploring the cancer epigenome—biological and translational implications
Baylin, S. B., & Jones, P. A. (2011) · Nature Reviews Cancer · doi:10.1038/nrc3130 · Cited by 2,871 · see citing works
Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA
He, Y., Li, B.-Z., Li, Z., Liu, P., Wang, Y., Tang, Q., Ding, J., Jia, Y., Chen, Z., Li, L., et al. (2011) · Science · doi:10.1126/science.1210944 · Cited by 2,776 · see citing works
Function and information content of DNA methylation
Schübeler, D. (2015) · Nature · doi:10.1038/nature14192 · Cited by 2,060 · see citing works
TET-mediated active DNA demethylation: mechanism, function and beyond
Wu, X., & Zhang, Y. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.33 · Cited by 1,661 · see citing works
TET enzymes, TDG and the dynamics of DNA demethylation
Kohli, R. M., & Zhang, Y. (2013) · Nature · doi:10.1038/nature12750 · Cited by 1,623 · see citing works
DNA-binding factors shape the mouse methylome at distal regulatory regions
Stadler, M. B., Murr, R., Burger, L., Ivanek, R., Lienert, F., Schöler, A., Nimwegen, E. V., Wirbelauer, C., Oakeley, E. J., Gaidatzis, D., et al. (2011) · Nature · doi:10.1038/nature10716 · Cited by 1,383 · see citing works
Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation
Moran-Crusio, K., Reavie, L., Shih, A., Abdel-Wahab, O., Ndiaye-Lobry, D., Lobry, C., Figueroa, M. E., Vasanthakumar, A., Patel, J., Zhao, X., et al. (2011) · Cancer Cell · doi:10.1016/j.ccr.2011.06.001 · Cited by 1,339 · see citing works
Epigenetic Determinants of CancerPreprint
Baylin, S. B., & Jones, P. A. (2016) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a019505 · Cited by 1,363 · see citing works
Role of TET enzymes in DNA methylation, development, and cancer
Rasmussen, K. D., & Helin, K. (2016) · Genes & Development · doi:10.1101/gad.276568.115 · Cited by 1,040 · see citing works
Self-citationReversing DNA Methylation: Mechanisms, Genomics, and Biological Functions
Wu, H., & Zhang, Y. (2014) · Cell · doi:10.1016/j.cell.2013.12.019 · Cited by 1,065 · see citing works
Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome
Yu, M., Hon, G. C., Szulwach, K. E., Song, C., Zhang, L., Kim, A., Li, X., Dai, Q., Shen, Y., Park, B., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.027 · Cited by 1,022 · see citing works
Transcriptional and epigenetic mechanisms of addiction
Robison, A. J., & Nestler, E. J. (2011) · Nature Reviews Neuroscience · doi:10.1038/nrn3111 · Cited by 993 · see citing works
The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells
Seisenberger, S., Andrews, S., Krueger, F., Arand, J., Walter, J., Santos, F., Popp, C., Thienpont, B., Dean, W., & Reik, W. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.11.001 · Cited by 973 · see citing works
A unique regulatory phase of DNA methylation in the early mammalian embryo
Smith, Z. D., Chan, M. M., Mikkelsen, T. S., Gu, H., Gnirke, A., Regev, A., & Meissner, A. (2012) · Nature · doi:10.1038/nature10960 · Cited by 964 · see citing works
DNA Methylation in MammalsPreprint
Li, E., & Zhang, Y. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a019133 · Cited by 952 · see citing works
Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution
Booth, M. J., Branco, M. R., Ficz, G., Oxley, D., Krueger, F., Reik, W., & Balasubramanian, S. (2012) · Science · doi:10.1126/science.1220671 · Cited by 923 · see citing works
TETonic shift: biological roles of TET proteins in DNA demethylation and transcription
Pastor, W. A., Aravind, L., & Rao, A. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3589 · Cited by 897 · see citing works
Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells
Blaschke, K., Ebata, K. T., Karimi, M. M., Zepeda-Martínez, J. A., Goyal, P., Mahapatra, S., Tam, A., Laird, D. J., Hirst, M., Rao, A., et al. (2013) · Nature · doi:10.1038/nature12362 · Cited by 865 · see citing works
Shen, L., Shao, N., Liu, X., & Nestler, E. J. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-284 · Cited by 852 · see citing works
5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging
Szulwach, K. E., Li, X., Li, Y., Song, C., Wu, H., Dai, Q., Irier, H. A., Upadhyay, A. K., Gearing, M., Levey, A. I., et al. (2011) · Nature Neuroscience · doi:10.1038/nn.2959 · Cited by 819 · see citing works
Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6
Zhang, Q., Zhao, K., Shen, Q., Han, Y., Gu, Y., Li, X., Zhao, D., Liu, Y., Wang, C., Zhang, X., et al. (2015) · Nature · doi:10.1038/nature15252 · Cited by 807 · see citing works
Uncovering the role of 5-hydroxymethylcytosine in the epigenome
Branco, M. R., Ficz, G., & Reik, W. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3080 · Cited by 766 · see citing works
Histone Methylation by PRC2 Is Inhibited by Active Chromatin Marks
Schmitges, F. W., Prusty, A. B., Faty, M., Stützer, A., Lingaraju, G. M., Aiwazian, J., Sack, R., Heß, D., Li, L., Zhou, S., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.03.025 · Cited by 725 · see citing works
Bhutani, N., Burns, D. M., & Blau, H. M. (2011) · Cell · doi:10.1016/j.cell.2011.08.042 · Cited by 688 · see citing works
Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidationPreprint
Wu, H., & Zhang, Y. (2011) · Genes & Development · doi:10.17615/800j-yk16 · Cited by 665 · see citing works
Tumour hypoxia causes DNA hypermethylation by reducing TET activity
Thienpont, B., Steinbacher, J., Zhao, H., D’Anna, F., Kuchnio, A., Ploumakis, A., Ghesquière, B., Van Dyck, L., Boeckx, B., Schoonjans, L., et al. (2016) · Nature · doi:10.1038/nature19081 · Cited by 635 · see citing works
Epigenomic alterations define lethal CIMP-positive ependymomas of infancy
Mack, S. C., Witt, H., Piro, R. M., Gu, L., Zuyderduyn, S., Stütz, A. M., Wang, X., Gallo, M., Garzia, L., Zayne, K., et al. (2014) · Nature · doi:10.1038/nature13108 · Cited by 607 · see citing works
Target analysis by integration of transcriptome and ChIP-seq data with BETA
Wang, S., Sun, H., Ma, J., Zang, C., Wang, C., Wang, J., Tang, Q., Meyer, C. A., Zhang, Y., & Liu, X. S. (2013) · Nature Protocols · doi:10.1038/nprot.2013.150 · Cited by 544 · see citing works
5-Hydroxymethylcytosine is a predominantly stable DNA modification
Bachman, M., Uribe‐Lewis, S., Yang, X., Williams, M., Murrell, A., & Balasubramanian, S. (2014) · Nature Chemistry · doi:10.1038/nchem.2064 · Cited by 554 · see citing works
Rivera, C. M., & Ren, B. (2013) · Cell · doi:10.1016/j.cell.2013.09.011 · Cited by 550 · see citing works
Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming
Song, C., Szulwach, K. E., Dai, Q., Fu, Y., Mao, S.-Q., Lin, L., Street, C., Li, Y., Poidevin, M., Wu, H., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.001 · Cited by 545 · see citing works
Guo, S., Diep, D. H., Plongthongkum, N., Fung, H.-L., Zhang, K., & Zhang, K. (2017) · Nature Genetics · doi:10.1038/ng.3805 · Cited by 516 · see citing works
Dawlaty, M. M., Ganz, K., Powell, B. E., Hu, Y.-C., Markoulaki, S., Cheng, A. W., Gao, Q., Kim, J., Choi, S.-W., Page, D. C., et al. (2011) · Cell stem cell · doi:10.1016/j.stem.2011.07.010 · Cited by 508 · see citing works
TET2 promotes histone O-GlcNAcylation during gene transcription
Chen, Q., Chen, Y., Bian, C., Fujiki, R., & Yu, X. (2012) · Nature · doi:10.1038/nature11742 · Cited by 523 · see citing works
Maeder, M. L., Angstman, J. F., Richardson, M. E., Linder, S. J., Cascio, V. M., Tsai, S. Q., Ho, Q. V., Sander, J. D., Reyon, D., Bernstein, B., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2726 · Cited by 498 · see citing works
Epigenetics: The link between nature and nurture
Tammen, S. A., Friso, S., & Choi, S. (2012) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2012.07.018 · Cited by 498 · see citing works
Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics
Shen, L., Wu, H., Diep, D., Yamaguchi, S., D’Alessio, A. C., Fung, H.-L., Zhang, K., & Zhang, Y. (2013) · Cell · doi:10.1016/j.cell.2013.04.002 · Cited by 497 · see citing works
Regulation of transposable elements by DNA modifications
Deniz, Ö., Frost, J. M., & Branco, M. R. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0106-6 · Cited by 480 · see citing works
TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS
Deplus, R., Delatte, B., Schwinn, M. K., Defrance, M., Méndez, J., Murphy, N., Dawson, M. A., Volkmar, M., Putmans, P., Calonne, E., et al. (2013) · The EMBO Journal · doi:10.1038/emboj.2012.357 · Cited by 488 · see citing works
The Discovery of 5‐Formylcytosine in Embryonic Stem Cell DNA
Pfaffeneder, T., Hackner, B., Truß, M., Münzel, M., Müller, M., Deiml, C. A., Hagemeier, C., & Carell, T. (2011) · Angewandte Chemie International Edition · doi:10.1002/anie.201103899 · Cited by 483 · see citing works
Glucose-regulated phosphorylation of TET2 by AMPK reveals a pathway linking diabetes to cancer
Wu, D., Hu, D., Chen, H., Shi, G., Fetahu, I. S., Wu, F., Rabidou, K., Fang, R., Tan, L., Xu, S., et al. (2018) · Nature · doi:10.1038/s41586-018-0350-5 · Cited by 477 · see citing works
Habibi, E., Brinkman, A. B., Arand, J., Kroeze, L. I., Kerstens, H. H. D., Matarese, F., Lepikhov, K., Gut, M., Heath, I. B., Hubner, N. C., et al. (2013) · Cell stem cell · doi:10.1016/j.stem.2013.06.002 · Cited by 470 · see citing works
PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos
Nakamura, T., Liu, Y.-J., Nakashima, H., Umehara, H., Inoue, K., Matoba, S., Tachibana, M., Ogura, A., Shinkai, Y., & Nakano, T. (2012) · Nature · doi:10.1038/nature11093 · Cited by 466 · see citing works
Crystal Structure of TET2-DNA Complex: Insight into TET-Mediated 5mC Oxidation
Hu, L., Li, Z., Cheng, J., Rao, Q., Gong, W., Liu, M., Shi, Y. G., Zhu, J., Wang, P., & Xu, Y. (2013) · Cell · doi:10.1016/j.cell.2013.11.020 · Cited by 448 · see citing works
Jin, S., Jiang, Y., Qiu, R., Rauch, T. A., Wang, Y., Schackert, G., Krex, D., Lü, Q., & Pfeifer, G. P. (2011) · Cancer Research · doi:10.1158/0008-5472.can-11-2023 · Cited by 441 · see citing works
Tet1 Is Critical for Neuronal Activity-Regulated Gene Expression and Memory Extinction
Rudenko, A., Dawlaty, M. M., Seo, J., Cheng, A. W., Meng, J., Le, T. T., Faull, K. F., Jaenisch, R., & Tsai, L. (2013) · Neuron · doi:10.1016/j.neuron.2013.08.003 · Cited by 435 · see citing works
Transcriptome-wide distribution and function of RNA hydroxymethylcytosine
Delatte, B., Wang, F., Ngoc, L. V., Collignon, É., Bonvin, E., Deplus, R., Calonne, E., Hassabi, B., Putmans, P., Awe, S., et al. (2016) · Science · doi:10.1126/science.aac5253 · Cited by 441 · see citing works
NANOG-dependent function of TET1 and TET2 in establishment of pluripotency
Costa, Y., Ding, J., Theunissen, T. W., Faiola, F., Hore, T. A., Shliaha, P. V., Fidalgo, M., Saunders, A., Lawrence, M., Dietmann, S., et al. (2013) · Nature · doi:10.1038/nature11925 · Cited by 433 · see citing works
Dawlaty, M. M., Breiling, A., Le, T. T., Raddatz, G., Barrasa, M. I., Cheng, A. W., Gao, Q., Powell, B. E., Li, Z., Xu, M., et al. (2013) · Developmental Cell · doi:10.1016/j.devcel.2012.12.015 · Cited by 431 · see citing works
Haffner, M. C., Chaux, A., Meeker, A. K., Esopi, D., Gerber, J. M., Pellakuru, L. G., Toubaji, A., Argani, P., Iacobuzio–Donahue, C. A., Nelson, W. G., et al. (2011) · Oncotarget · doi:10.18632/oncotarget.316 · Cited by 419 · see citing works
Primordial Germ Cells in MicePreprint
Saitou, M., & Yamaji, M. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a008375 · Cited by 418 · see citing works
Kaas, G. A., Zhong, C., Eason, D. E., Ross, D. L., Vachhani, R., Ming, G., King, J. R., Song, H., & Sweatt, J. D. (2013) · Neuron · doi:10.1016/j.neuron.2013.08.032 · Cited by 411 · see citing works
MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets
Shao, Z., Zhang, Y., Yuan, G., Orkin, S. H., & Waxman, D. J. (2012) · Genome biology · doi:10.1186/gb-2012-13-3-r16 · Cited by 402 · see citing works
Epigenetic reprogramming in mouse pre-implantation development and primordial germ cells
Saitou, M., Kagiwada, S., & Kurimoto, K. (2011) · Development · doi:10.1242/dev.050849 · Cited by 410 · see citing works
Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genesPreprint
Nestor, C. E., Ottaviano, R., Reddington, J. P., Sproul, D., Reinhardt, D., Dunican, D. S., Katz, E., Dixon, J. M., Harrison, D. J., & Meehan, R. R. (2011) · Genome Research · doi:10.1101/gr.126417.111 · Cited by 403 · see citing works
Chromatin Connections to Pluripotency and Cellular Reprogramming
Orkin, S. H., & Hochedlinger, K. (2011) · Cell · doi:10.1016/j.cell.2011.05.019 · Cited by 394 · see citing works
Yang, R., Qu, C., Zhou, Y., Konkel, J. E., Shi, S., Liu, Y., Chen, C., Liu, S., Liu, D., Yibu, C., et al. (2015) · Immunity · doi:10.1016/j.immuni.2015.07.017 · Cited by 392 · see citing works
The Role of DNA Methylation in Aging, Rejuvenation, and Age-Related Disease
Johnson, A. A., Akman, K., Calimport, S., Wuttke, D., Stolzing, A., & de Magalhães, J. P. (2012) · Rejuvenation Research · doi:10.1089/rej.2012.1324 · Cited by 386 · see citing works
Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2
Doege, C. A., Inoue, K., Yamashita, T., Rhee, D. B., Travis, S. N., Fujita, R., Guarnieri, P., Bhagat, G., Vanti, W. B., Shih, A. H., et al. (2012) · Nature · doi:10.1038/nature11333 · Cited by 382 · see citing works
Tet family proteins and 5-hydroxymethylcytosine in development and disease
Tan, L., & Shi, Y. G. (2012) · Development · doi:10.1242/dev.070771 · Cited by 377 · see citing works
Fbxl10/Kdm2b Recruits Polycomb Repressive Complex 1 to CpG Islands and Regulates H2A Ubiquitylation
Wu, X., Johansen, J. V., & Helin, K. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.016 · Cited by 375 · see citing works
Self-citationMethylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family
Baubec, T., Ivánek, R., Lienert, F., & Schübeler, D. (2013) · Cell · doi:10.1016/j.cell.2013.03.011 · Cited by 365 · see citing works
Tet1 Regulates Adult Hippocampal Neurogenesis and Cognition
Zhang, R.-R., Cui, Q., Murai, K., Lim, Y. C., Smith, Z. D., Jin, S., Ye, P., Rosa, L., Lee, Y. K., Wu, H.-P., et al. (2013) · Cell stem cell · doi:10.1016/j.stem.2013.05.006 · Cited by 361 · see citing works
Mechanism and Function of Oxidative Reversal of DNA and RNA Methylation
Shen, L., Song, C., He, C., & Zhang, Y. (2014) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060713-035513 · Cited by 359 · see citing works
Loss of Tet Enzymes Compromises Proper Differentiation of Embryonic Stem Cells
Dawlaty, M. M., Breiling, A., Le, T., Barrasa, M. I., Raddatz, G., Gao, Q., Powell, B. E., Cheng, A. W., Faull, K. F., Lyko, F., et al. (2014) · Developmental Cell · doi:10.1016/j.devcel.2014.03.003 · Cited by 338 · see citing works
Hon, G. C., Song, C., Du, T., Jin, F., Selvaraj, S., Lee, A. Y., Yen, C., Ye, Z., Mao, S.-Q., Wang, B.-A., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.08.026 · Cited by 332 · see citing works
Vella, P., Scelfo, A., Jammula, S., Chiacchiera, F., Williams, K., Cuomo, A., Roberto, A., Christensen, J. F., Bonaldi, T., Helin, K., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2012.12.019 · Cited by 327 · see citing works
Self-citationVitamin C modulates TET1 function during somatic cell reprogramming
Chen, J., Guo, L., Zhang, L., Wu, H., Yang, J., Liu, H., Wang, X., Hu, X., Gu, T., Zhou, Z., et al. (2013) · Nature Genetics · doi:10.1038/ng.2807 · Cited by 319 · see citing works
DNA methylation dynamics during the mammalian life cycle
Hackett, J. A., & Surani, M. A. (2012) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2011.0328 · Cited by 317 · see citing works
DNA methylation: TET proteins—guardians of CpG islands?
Williams, K., Christensen, J. F., & Helin, K. (2011) · EMBO Reports · doi:10.1038/embor.2011.233 · Cited by 315 · see citing works
Self-citationFetahu, I. S., Höbaus, J., & Kállay, E. (2014) · Frontiers in Physiology · doi:10.3389/fphys.2014.00164 · Cited by 313 · see citing works
Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA
Pfaffeneder, T., Spada, F., Wagner, M., Brandmayr, C., Laube, S. K., Eisen, D., Truß, M., Steinbacher, J., Hackner, B., Kotljarova, O., et al. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1532 · Cited by 306 · see citing works
Tet1 controls meiosis by regulating meiotic gene expression
Yamaguchi, S., Hong, K., Liu, R., Shen, L., Inoue, A., Diep, D. H., Zhang, K., & Zhang, Y. (2012) · Nature · doi:10.1038/nature11709 · Cited by 307 · see citing works
WT1 Recruits TET2 to Regulate Its Target Gene Expression and Suppress Leukemia Cell Proliferation
Wang, Y., Xiao, M., Chen, X., Chen, L., Xu, Y., Lv, L., Wang, P., Yang, H., Ma, S., Lin, H., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2014.12.023 · Cited by 304 · see citing works
Gertz, J., Varley, K. E., Reddy, T. E., Bowling, K. M., Pauli, F., Parker, S. L., Kucera, K. S., Willard, H. F., & Myers, R. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002228 · Cited by 304 · see citing works
Wen, L., Li, X., Yan, L., Tan, Y., Li, R., Zhao, Y., Wang, Y., Xie, J., Zhang, Y., Song, C., et al. (2014) · Genome biology · doi:10.1186/gb-2014-15-3-r49 · Cited by 288 · see citing works
The Ten-Eleven Translocation-2 (TET2) gene in hematopoiesis and hematopoietic diseases
Solary, É., Bernard, O., Tefferi, A., Fuks, F., & Vainchenker, W. (2013) · Leukemia · doi:10.1038/leu.2013.337 · Cited by 284 · see citing works
Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells
Szulwach, K. E., Li, X., Li, Y., Song, C., Han, J. W., Kim, S., Namburi, S., Hermetz, K. E., Kim, J. J., Rudd, M. K., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002154 · Cited by 288 · see citing works
TET1 Suppresses Cancer Invasion by Activating the Tissue Inhibitors of Metalloproteinases
Hsu, C.-H., Peng, K.-L., Kang, M.-L., Chen, Y.-R., Yang, Y., Tsai, C.-H., Chu, C.-S., Jeng, Y., Chen, Y.-T., Lin, F.-M., et al. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.030 · Cited by 280 · see citing works
Loss of 5‐hydroxymethylcytosine is accompanied with malignant cellular transformation
Kudo, Y., Tateishi, K., Yamamoto, K., Yamamoto, S., Asaoka, Y., Ijichi, H., Nagae, G., Yoshida, H., Aburatani, H., & Koike, K. (2012) · Cancer Science · doi:10.1111/j.1349-7006.2012.02213.x · Cited by 278 · see citing works
TET (Ten-eleven translocation) family proteins: structure, biological functions and applications
Zhang, X., Zhang, Y., Wang, C., & Wang, X. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01537-x · Cited by 286 · see citing works
HMGA2/TET1/HOXA9 signaling pathway regulates breast cancer growth and metastasis
Sun, M., Song, C., Huang, H., Frankenberger, C. A., Sankarasharma, D., Gomes, S., Chen, P., Chen, J., Chada, K. K., He, C., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1305172110 · Cited by 273 · see citing works
Epigenetic reprogramming enables the transition from primordial germ cell to gonocyte
Hill, P. W. S., Leitch, H. G., Requena, C. E., Sun, Z., Amouroux, R., Roman-Trufero, M., Borkowska, M., Terragni, J., Vaisvila, R., Linnett, S., et al. (2018) · Nature · doi:10.1038/nature25964 · Cited by 272 · see citing works
Rasmussen, K. D., Jia, G., Johansen, J. V., Pedersen, M. T., Rapin, N., Bagger, F. O., Porse, B. T., Bernard, O. A., Christensen, J., & Helin, K. (2015) · Genes & Development · doi:10.1101/gad.260174.115 · Cited by 270 · see citing works
Self-citationThe Dynamics of DNA Methylation in Schizophrenia and Related Psychiatric Disorders
Grayson, D. R., & Guidotti, A. (2012) · Neuropsychopharmacology · doi:10.1038/npp.2012.125 · Cited by 267 · see citing works
Role of Tet proteins in enhancer activity and telomere elongationPreprint
Lu, F., Liu, Y., Jiang, L., Yamaguchi, S., & Zhang, Y. (2014) · Genes & Development · doi:10.1101/gad.248005.114 · Cited by 269 · see citing works
Xu, Y., Xu, C., Kato, A., Tempel, W., Abreu, J. G., Bian, C., Hu, Y., Hu, D., Zhao, B., Cerovina, T., et al. (2012) · Cell · doi:10.1016/j.cell.2012.11.014 · Cited by 271 · see citing works
Advances in the profiling of DNA modifications: cytosine methylation and beyond
Plongthongkum, N., Diep, D. H., & Zhang, K. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3772 · Cited by 259 · see citing works
Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells
Huang, Y., Chávez, L., Chang, X., Wang, X., Pastor, W. A., Kang, J., Zepeda-Martínez, J. A., Pape, U. J., Jacobsen, S. E., Peters, B., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1322921111 · Cited by 258 · see citing works
Zhang, X., Su, J., Jeong, M., Ko, M., Huang, Y., Park, H. J., Guzman, A., Lei, Y., Huang, Y.-H., Rao, A., et al. (2016) · Nature Genetics · doi:10.1038/ng.3610 · Cited by 258 · see citing works
Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine
Yu, M., Hon, G. C., Szulwach, K. E., Song, C., Jin, P., Ren, B., & He, C. (2012) · Nature Protocols · doi:10.1038/nprot.2012.137 · Cited by 250 · see citing works
5‐Hydroxymethylcytosine, the Sixth Base of the Genome
Münzel, M., Globisch, D., & Carell, T. (2011) · Angewandte Chemie International Edition · doi:10.1002/anie.201101547 · Cited by 252 · see citing works
DNA methylation: A mechanism for embedding early life experiences in the genome
Szyf, M., & Bick, J. (2013) · Child Development · doi:10.1111/j.1467-8624.2012.01793.x · Cited by 251 · see citing works
ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection
Long, H. K., Blackledge, N. P., & Klose, R. J. (2013) · Biochemical Society Transactions · doi:10.1042/bst20130028 · Cited by 243 · see citing works
Common stemness regulators of embryonic and cancer stem cells
Hadjimichael, C. (2015) · World Journal of Stem Cells · doi:10.4252/wjsc.v7.i9.1150 · Cited by 246 · see citing works
Methyl Donor Micronutrients that Modify DNA Methylation and Cancer Outcome
Mahmoud, A. M., & Ali, M. M. (2019) · Nutrients · doi:10.3390/nu11030608 · Cited by 249 · see citing works
Active DNA demethylation at enhancers during the vertebrate phylotypic period
Bogdanović, O., Smits, A. H., de la Calle‐Mustienes, E., Tena, J. J., Ford, E., Williams, R. M., Senanayake, U., Schultz, M. D., Hontelez, S., van Kruijsbergen, I., et al. (2016) · Nature Genetics · doi:10.1038/ng.3522 · Cited by 231 · see citing works
Early life adversity and the epigenetic programming of hypothalamic-pituitary-adrenal function
Anacker, C., O'Donnell, K. J., & Meaney, M. J. (2014) · Dialogues in Clinical Neuroscience · doi:10.31887/dcns.2014.16.3/canacker · Cited by 237 · see citing works
- Authors
- Williams, K., Christensen, J., Pedersen, M. T., Johansen, J. V., Cloos, P. A. C., Rappsilber, J., & Helin, K.
- Affiliations
- University of Copenhagen (DK)
- Wellcome Centre for Cell Biology (GB)
- Corresponding author
- Helin, Kristian
- ORCID
- Venue
- Nature
- Published
- 2011-04-13
- Volume
- 473
- Issue
- 7347
- Pages
- 343-348
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3408592
- OpenAlex
- W2014623973
- Cited by
- 1,021
- References
- 30
- Citations by year
- 2026: 23 · 2025: 29 · 2024: 29 · 2023: 37 · 2022: 44 · 2021: 57 · 2020: 49 · 2019: 55 · 2018: 63 · 2017: 65 · 2016: 87 · 2015: 72 · 2014: 108 · 2013: 125 · 2012: 114
- FWCI
- 53.32
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Funders
- Wellcome Trust (084229)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
- Keywords
- TET1, 5-hydroxymethylcytosine, DNA demethylation, transcription start sites, transcriptional repression, mouse embryonic stem cells, TET enzymes, genome-wide binding sites
- MeSH terms
- DNA (Cytosine-5-)-Methyltransferase 1, Animals, Cell Line, Cytosine, DNA (Cytosine-5-)-Methyltransferases, DNA-Binding Proteins, Protein Binding, Proto-Oncogene Proteins, Repressor Proteins, Transcription, Genetic, Down-Regulation, CpG Islands, DNA Methylation, Transcription Initiation Site, 5-Methylcytosine, Mice, Embryonic Stem Cells, Gene Knockdown Techniques, Sin3 Histone Deacetylase and Corepressor Complex
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