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Role of TET enzymes in DNA methylation, development, and cancer
Open accessAbstract
The pattern of DNA methylation at cytosine bases in the genome is tightly linked to gene expression, and DNA methylation abnormalities are often observed in diseases. The ten eleven translocation (TET) enzymes oxidize 5-methylcytosines (5mCs) and promote locus-specific reversal of DNA methylation. TET genes, and especially TET2 , are frequently mutated in various cancers, but how the TET proteins contribute to prevent the onset and maintenance of these malignancies is largely unknown. Here, we highlight recent advances in understanding the physiological function of the TET proteins and their role in regulating DNA methylation and transcription. In addition, we discuss some of the key outstanding questions in the field.
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“Generally, 2OGO catalyze specific hydroxylation of substrates, which, in turn, leads to demethylations via other catalytic cycles or downstream pathway involving thymine-DNA-glycosylase, which catalyzed base excision with DNA base excision repair [101,120].”
From Vitamin C-Sources, Physiological Role, Kinetics, Deficiency, Use, Toxicity, and Determination (2021) · cites this paper as [120]
Experimental — accuracy not yet measuredIn the citing paper
“TET2 is frequently mutated or lost somatically in both myeloid and lymphoid malignancies63,64.”
From Targeting cancer vulnerabilities with high-dose vitamin C (2019) · cites this paper as [63]
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“Thus, it was remarkable when ten eleven translocation protein 1 (TET1) was discovered and shown to be able to modify methylcytosine and potentially erase DNAmethylation (Tahiliani et al. 2009).”
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Ito, S., Shen, L., Dai, Q., Wu, S. C., Collins, L. B., Swenberg, J. A., He, C., & Zhang, Y. (2011) · Science · doi:10.1126/science.1210597 · Cited by 3,451 · cited 3×
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The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain
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“By comparison, the products of further TET-mediated oxidation, 5fC and 5caC, are observed at ∼10-fold to 100-fold lower levels than 5hmC and often close to or under the detection limit (Kriaucionis and Heintz 2009; Globisch et al. 2010; Szwagierczak et al. 2010; He et al. 2011; Ito et al. 2011; Pfaffeneder et al. 2011…”
BackgroundIdentification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma
Noushmehr, H., Weisenberger, D. J., Diefes, K., Phillips, H. S., Pujara, K., Berman, B. P., Pan, F., Pelloski, C. E., Sulman, E. P., Bhat, K. P., et al. (2010) · Cancer Cell · doi:10.1016/j.ccr.2010.03.017 · Cited by 2,337 · cited 1×
“Accordingly, neomorphic IDH1mutations that result in high levels of 2-HG and impairment of TET enzymes in gliomas are tightly associated with aberrant DNA hypermethylation (Noushmehr et al. 2010; Turcan et al. 2012).”
BackgroundIDH1 mutation is sufficient to establish the glioma hypermethylator phenotype
Turcan, S., Rohle, D., Goenka, A., Walsh, L. A., Fang, F., Yilmaz, E., Campos, C., Fabius, A. W. M., Lu, C., Ward, P. S., et al. (2012) · Nature · doi:10.1038/nature10866 · Cited by 1,974 · cited 3×
“Nonetheless, decreased expression of TET proteins and lower 5hmC levels are general hallmarks of many cancer types, including gastric, prostate, liver, lung, and breast cancer as well as glioblastoma and melanoma (Kudo et al. 2012; Lian et al. 2012; Turcan et al. 2012; Liu et al. 2013a; Yang et al. 2013).”
Age-related mutations associated with clonal hematopoietic expansion and malignancies
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“Although the increase in DNAmethylation was rather modest, this study suggests that Tet2 is important for establishing the DNAhypomethylated state of tissue-specific enhancers during development of neuronal tissues (Lister et al. 2013).”
BackgroundMutation in TET2 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 · cited 2×
“In contrast, the TET2 gene was independently unearthed in a study of myelodysplastic syndrome (MDS) and AML patients with 4q24 alterations, where it was the only ORF found in a minimally deleted region (Delhommeau et al. 2009; Langemeijer et al. 2009).”
BackgroundResultDNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA
Ooi, S. K. T., Qiu, C., Bernstein, E., Li, K., Jia, D., Yang, Z., Erdjument‐Bromage, H., Tempst, P., Lin, S., Allis, C. D., et al. (2007) · Nature · doi:10.1038/nature05987 · Cited by 1,648 · cited 1×
“2011b) and the exclusion of de novo DNA methyltransferases by H3K4me3 methylation (Ooi et al. 2007; Otani et al. 2009; Guo et al. 2015; Noh et al. 2015).”
BackgroundClinical Effect of Point Mutations in Myelodysplastic Syndromes
Bejar, R., Stevenson, K., Abdel-Wahab, O., Galili, N., Nilsson, B., Garcia-Manero, G., Kantarjian, H., Raza, A., Levine, R. L., Neuberg, D., et al. (2011) · New England Journal of Medicine · doi:10.1056/nejmoa1013343 · Cited by 1,627
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“Accordingly, with statistical significance, TET2 mutations are associated with SF3B1, ZRSR2, and ASXL1 mutations in MDS patients (Haferlach et al. 2014); STAG2, DNAH9, and serine–threonine kinasemutations inAML patients (CancerGenome Atlas Research Network 2013); and RHOA, IDH2, and DNMT3A mutations in AITL patients (…”
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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
Charting a dynamic DNA methylation landscape of the human genome
Ziller, M. J., Gu, H., Müller, F., Donaghey, J., Tsai, L. T.-Y., Kohlbacher, O., De Jager, P. L., Rosen, E. D., Bennett, D. A., Bernstein, B. E., et al. (2013) · Nature · doi:10.1038/nature12433 · Cited by 1,357 · cited 2×
“Thus, in contrast to a relatively static DNAmethylation environment, the gain and loss of DNA methylation at regulatory regions are prominent features of normal development (Hon et al. 2013; Ziller et al. 2013).”
BackgroundImpaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2
Ko, M., Huang, Y., Jankowska, A. M., Pape, U. J., Tahiliani, M., Bandukwala, H. S., An, J., Lamperti, E. D., Koh, K. P., Ganetzky, R. D., et al. (2010) · Nature · doi:10.1038/nature09586 · Cited by 1,340
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 · cited 3×
“Loss of Tet2 results in age-associated extramedullary hematopoiesis and expansion of monocytes and granulocytes in the spleen (Ko et al. 2011; Li et al. 2011; Moran-Crusio et al. 2011; Quivoron et al. 2011; Shide et al. 2012), whereas Tet1 deficiency leads to an overall lymphoid bias and dysregulated B-cell lineage di…”
BackgroundXiao, M., Yang, H., Xu, W., Ma, S., Lin, H., Zhu, H., Liu, L., Liu, Y., Yang, C., Xu, Y., et al. (2012) · Genes & Development · doi:10.1101/gad.191056.112 · Cited by 1,188
The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes
Gu, T., Guo, F., Yang, H., Wu, H.-P., Xu, G., Liu, W., Xie, Z.-G., Shi, L., He, X., Jin, S., et al. (2011) · Nature · doi:10.1038/nature10443 · Cited by 1,144
Reversing 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
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 1,050
TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity
Williams, K., Christensen, J., Pedersen, M. T., Johansen, J. V., Cloos, P. A. C., Rappsilber, J., & Helin, K. (2011) · Nature · doi:10.1038/nature10066 · Cited by 1,021 · cited 3×
“In addition, in vivo chromatin immunoprecipitation of Tet1 shows that it is highly enriched on CpG islands, most of which are associated with promoters with intermediate and high CpG content, and that this enrichment is lost upon introduction of amutation in the CXXC domain (Williams et al. 2011; Wu et al. 2011b; Xu e…”
BackgroundResultSelf-citationDynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives
Spruijt, C. G., Gnerlich, F., Smits, A. H., Pfaffeneder, T., Jansen, P. W. T. C., Bauer, C., Münzel, M., Wagner, M., Müller, M., Khan, F., et al. (2013) · Cell · doi:10.1016/j.cell.2013.02.004 · Cited by 973 · cited 3×
“Instead, the much less abundant cytosine species 5fC and 5caC appear to interact with numerous proteins, including TDG, p53, DNA repair factors, chromatin remodeling factors, and forkhead box TFs (Iurlaro et al. 2013; Spruijt et al. 2013).”
BackgroundQuivoron, C., Couronné, L., Della Valle, V., Lopez, C. K., Plo, I., Wagner-Ballon, O., Do Cruzeiro, M., Delhommeau, F., Arnulf, B., Stern, M.-H., et al. (2011) · Cancer Cell · doi:10.1016/j.ccr.2011.06.003 · Cited by 924 · cited 4×
“This is further accompanied by a gradual expansion of myeloid-biased HSCs in Tet2-deficient mice versus lymphoid-primed multipotent progenitors (LMPPs) in Tet1 mutant mice, thus reflecting an early skewing of myeloid or lymphoid differentiation (Quivoron et al. 2011; Cimmino et al. 2015).”
BackgroundInfluentialVitamin 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
Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates
Globisch, D., Münzel, M., Müller, M., Michalakis, S., Wagner, M., Koch, S., Brückl, T., Biel, M., & Carell, T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015367 · Cited by 865
Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis
Busque, L., Patel, J. P., Figueroa, M. E., Vasanthakumar, A., Provost, S., Hamilou, Z., Mollica, L., Li, J., Viale, A., Heguy, A., et al. (2012) · Nature Genetics · doi:10.1038/ng.2413 · Cited by 830 · cited 1×
“Second, TET2 mutations are frequently observed in aged healthy individuals with clonal hematopoiesis and increase the propensity to develop hematopoieticmalignancies (Busque et al. 2012; Genovese et al. 2014; Jaiswal et al. 2014; Xie et al. 2014).”
BackgroundThymine DNA Glycosylase Can Rapidly Excise 5-Formylcytosine and 5-Carboxylcytosine
Maiti, A., & Drohat, A. C. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.c111.284620 · Cited by 825
Cortellino, S., Xu, J., Sannai, M., Moore, R., Caretti, E., Cigliano, A., Le Coz, M., Devarajan, K., Wessels, A., Soprano, D., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.020 · Cited by 809
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 · cited 1×
“induced stimulation in a histone deacetylase (HDAC)-dependent manner (Zhang et al. 2015).”
BackgroundGenome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
Pastor, W. A., Pape, U. J., Huang, Y., Henderson, H. R., Lister, R., Ko, M., McLoughlin, E. M., Brudno, Y., Mahapatra, S., Kapranov, P., et al. (2011) · Nature · doi:10.1038/nature10102 · Cited by 804 · cited 1×
“There has been substantial interest inmapping cytosine oxidation products in the genome with the aim of understanding their role in gene regulation and DNA methylation dynamics (Pastor et al. 2011; Stroud et al. 2011; Szulwach et al. 2011; Williams et al. 2011; Wu et al. 2011a; Xu et al. 2011c; Sérandour et al. 2012).”
BackgroundRethinking how DNA methylation patterns are maintained
Jones, P. A., & Liang, G. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2651 · Cited by 799
Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma
Lian, C. G., Xu, Y., Ceol, C., Wu, F., Larson, A., Dresser, K., Xu, W., Tan, L., Hu, Y., Zhan, Q., et al. (2012) · Cell · doi:10.1016/j.cell.2012.07.033 · Cited by 789 · cited 1×
“Nonetheless, decreased expression of TET proteins and lower 5hmC levels are general hallmarks of many cancer types, including gastric, prostate, liver, lung, and breast cancer as well as glioblastoma and melanoma (Kudo et al. 2012; Lian et al. 2012; Turcan et al. 2012; Liu et al. 2013a; Yang et al. 2013).”
BackgroundAcquired mutations in TET2 are common in myelodysplastic syndromes
Langemeijer, S. M. C., Kuiper, R. P., Berends, M., Knops, R., Aslanyan, M. G., Massop, M., Stevens-Linders, E., van Hoogen, P., van Kessel, A. G., Raymakers, R. A. P., et al. (2009) · Nature Genetics · doi:10.1038/ng.391 · Cited by 755
Chen, T., Ueda, Y., Dodge, J. E., Wang, Z., & Li, E. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.16.5594-5605.2003 · Cited by 751
Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia
Jan, M., Snyder, T. M., Corces-Zimmerman, M. R., Vyas, P., Weissman, I. L., Quake, S. R., & Majeti, R. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3004315 · Cited by 721 · cited 1×
“First, TET2 mutations can be found in premalignant HSCs in MDS and AML patients and are preserved in the tumor bulk along with additional oncogenic mutations (Jan et al. 2012; Chan and Majeti 2013; Itzykson et al. 2013).”
BackgroundLi, Z., Cai, X., Cai, C.-L., Wang, J., Zhang, W., Petersen, B. E., Yang, F.-C., & Xu, M. (2011) · Blood · doi:10.1182/blood-2010-12-325241 · Cited by 671 · cited 1×
“Loss of Tet2 results in age-associated extramedullary hematopoiesis and expansion of monocytes and granulocytes in the spleen (Ko et al. 2011; Li et al. 2011; Moran-Crusio et al. 2011; Quivoron et al. 2011; Shide et al. 2012), whereas Tet1 deficiency leads to an overall lymphoid bias and dysregulated B-cell lineage di…”
BackgroundSomatic RHOA mutation in angioimmunoblastic T cell lymphoma
Sakata‐Yanagimoto, M., Enami, T., Yoshida, K., Shiraishi, Y., Ishii, R., Miyake, Y., Muto, H., Tsuyama, N., Sato‐Otsubo, A., Okuno, Y., et al. (2014) · Nature Genetics · doi:10.1038/ng.2872 · Cited by 667 · cited 1×
“2014); STAG2, DNAH9, and serine–threonine kinasemutations inAML patients (CancerGenome Atlas Research Network 2013); and RHOA, IDH2, and DNMT3A mutations in AITL patients (Palomero et al. 2014; Sakata-Yanagimoto et al. 2014).”
BackgroundXu, Y., Wu, F., Tan, L., Kong, L., Xiong, L., Deng, J., Barbera, A. J., Zheng, L., Zhang, H., Huang, S., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.04.005 · Cited by 647
Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells
Wu, H., D’Alessio, A. C., Ito, S., Xia, K., Wang, Z., Cui, K., Zhao, K., Eve Sun, Y., & Zhang, Y. (2011) · Nature · doi:10.1038/nature09934 · Cited by 646
Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas
Palomero, T., Couronné, L., Khiabanian, H., Kim, M., Ambesi‐Impiombato, A., Pérez-García, A., Carpenter, Z., Abate, F., Allegretta, M., Haydu, J. E., et al. (2014) · Nature Genetics · doi:10.1038/ng.2873 · Cited by 636 · cited 1×
“2014); STAG2, DNAH9, and serine–threonine kinasemutations inAML patients (CancerGenome Atlas Research Network 2013); and RHOA, IDH2, and DNMT3A mutations in AITL patients (Palomero et al. 2014; Sakata-Yanagimoto et al. 2014).”
BackgroundKo, M., Bandukwala, H. S., An, J., Lamperti, E. D., Thompson, E. C., Hastie, R., Tsangaratou, A., Rajewsky, K., Koralov, S. B., & Rao, A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1112317108 · Cited by 616
Yin, R., Mao, S.-Q., Zhao, B., Chong, Z., Yang, Y., Zhao, C., Zhang, D., Huang, H., Gao, J., Li, Z., et al. (2013) · Journal of the American Chemical Society · doi:10.1021/ja4028346 · Cited by 609 · cited 3×
“Although the precisemechanism is unknown, it is likely that vitaminC interacts directly with the catalytic domain of TET proteins and provides a local reducing environment that increases recycling efficiency of the Fe(II) cofactor (Yin et al. 2013).”
BackgroundWu, H., D’Alessio, A. C., Ito, S., Wang, Z., 崔凯荣, Zhao, K., Sun, Y. E., & Zhang, Y. (2011) · Genes & Development · doi:10.1101/gad.2036011 · Cited by 603
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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 577
TET2 mutations predict response to hypomethylating agents in myelodysplastic syndrome patients
Bejar, R. L., Lord, A. M., Stevenson, K. E., Bar‐Natan, M., Pérez-Ladaga, A., Zaneveld, J. E., Wang, H., Caughey, B. A., Stojanov, P., Getz, G. A., et al. (2014) · Blood · doi:10.1182/blood-2014-06-582809 · Cited by 575 · cited 1×
“Therapeutic intervention against this early aberration in AML, MDS, and CMML patients using demethylating agents (azacytidine and decitabine) have yielded inconclusive results (Braun et al. 2011; Itzykson et al. 2011; Bejar et al. 2014; Meldi et al. 2015).”
What a difference a hydroxyl makes: mutant IDH, (R)-2-hydroxyglutarate, and cancer
Losman, J.-A., & Kaelin, W. G. (2013) · Genes & Development · doi:10.1101/gad.217406.113 · Cited by 570
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 562
Programming and Inheritance of Parental DNA Methylomes in Mammals
Wang, L., Zhang, J., Duan, J., Gao, X., Zhu, W. Z., Lu, X., Yang, L., Zhang, J., Li, G., Ci, W., et al. (2014) · Cell · doi:10.1016/j.cell.2014.04.017 · Cited by 556 · cited 2×
“2014), and Tet3mediated cytosine oxidation in the developing embryo occurs at a wide range of genomic elements (Wang et al. 2014).”
BackgroundTET2 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 537 · cited 1×
“Although several genome-wide data sets have been published (Chen et al. 2013; Deplus et al. 2013), none of themhave systematically tested signal specificity.”
BackgroundTET2 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 508 · cited 1×
“Although several genome-wide data sets have been published (Chen et al. 2013; Deplus et al. 2013), none of themhave systematically tested signal specificity.”
BackgroundDawlaty, 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 · cited 1×
“2015), whereas deletions of either Tet1 (Dawlaty et al. 2011) or Tet2 (Moran-Crusio et al.”
BackgroundValinluck, V., & Sowers, L. C. (2007) · Cancer Research · doi:10.1158/0008-5472.can-06-3123 · Cited by 502
Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation
Song, J., Rechkoblit, O., Bestor, T. H., & Patel, D. J. (2010) · Science · doi:10.1126/science.1195380 · Cited by 499 · cited 1×
“Structural studies of CXXC domains in other proteins (Cierpicki et al. 2010; Song et al. 2011; Xu et al. 2011a) have shown that these can bind to a single CpG site.”
BackgroundGenome-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
Song, S. J., Poliseno, L., Song, M. S., Ala, U., Webster, K. A., Ng, C., Beringer, G., Brikbak, N. J., Yuan, X., Cantley, L. C., et al. (2013) · Cell · doi:10.1016/j.cell.2013.06.026 · Cited by 496
5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells
Stroud, H., Feng, S., Kinney, S. R. M., Pradhan, S., & Jacobsen, S. E. (2011) · Genome biology · doi:10.1186/gb-2011-12-6-r54 · Cited by 490 · cited 1×
“There has been substantial interest inmapping cytosine oxidation products in the genome with the aim of understanding their role in gene regulation and DNA methylation dynamics (Pastor et al. 2011; Stroud et al. 2011; Szulwach et al. 2011; Williams et al. 2011; Wu et al. 2011a; Xu et al. 2011c; Sérandour et al. 2012).”
BackgroundThe 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 · cited 1×
“By comparison, the products of further TET-mediated oxidation, 5fC and 5caC, are observed at ∼10-fold to 100-fold lower levels than 5hmC and often close to or under the detection limit (Kriaucionis and Heintz 2009; Globisch et al. 2010; Szwagierczak et al. 2010; He et al. 2011; Ito et al. 2011; Pfaffeneder et al. 2011…”
BackgroundItzykson, R., Kosmider, O., Cluzeau, T., Mas, V. M., Dreyfus, F., Beyne‐Rauzy, O., Quesnel, B., Vey, N., Gelsi‐Boyer, V., Raynaud, S., et al. (2011) · Leukemia · doi:10.1038/leu.2011.71 · Cited by 480
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues
Hon, G. C., Rajagopal, N., Shen, Y., McCleary, D. F., Yue, F., Dang, M. D., & Ren, B. (2013) · Nature Genetics · doi:10.1038/ng.2746 · Cited by 477
Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation
Hashimoto, H., Liu, Y., Upadhyay, A. K., Chang, Y., Howerton, S. B., Vertino, P. M., Zhang, X., & Cheng, X. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks155 · Cited by 473 · cited 4×
“2003; Jones and Liang 2009), and these enzymes readily methylate a DNA substrate containing 5hmC (Hashimoto et al. 2012; Ji et al. 2014).”
BackgroundInfluentialCrystal 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 467 · cited 1×
“A comparison of crystal structures of human TET2 in complex with all three substrates indicates that the substrate preference is due to subtle differences in the catalytic cavity (Hu et al. 2013; 2015).”
BackgroundDynamics of 5-Hydroxymethylcytosine and Chromatin Marks in Mammalian Neurogenesis
Hahn, M. A., Qiu, R., Wu, X., Li, A. X., Zhang, H., Wang, J., Jui, J., Jin, S., Jiang, Y., Pfeifer, G. P., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.01.011 · Cited by 455 · cited 1×
“For instance, loss of Tet activity is associated with altered neuronal activity and has been implicated in learning and memory processes as well as cocaine addiction (Hahn et al. 2013; Rudenko et al. 2013; Feng et al. 2015).”
BackgroundNANOG-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 450 · cited 1×
“In addition, TET activity plays an important role in induced pluripotent stem cell formation (Doege et al. 2012; Costa et al. 2013) as well as smooth muscle cell differentiation (Liu et al.”
BackgroundDawlaty, 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 450 · cited 3×
“Moreover, in some cases, deletion of one or several of the TET enzymes can be compensated for by increased expression or activity of the other TET family members (Dawlaty et al. 2013).”
BackgroundInfluentialTet1 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 450
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 440 · cited 1×
“By comparison, the products of further TET-mediated oxidation, 5fC and 5caC, are observed at ∼10-fold to 100-fold lower levels than 5hmC and often close to or under the detection limit (Kriaucionis and Heintz 2009; Globisch et al. 2010; Szwagierczak et al. 2010; He et al. 2011; Ito et al. 2011; Pfaffeneder et al. 2011…”
BackgroundJin, S.-G., Kadam, S., & Pfeifer, G. P. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq223 · Cited by 437
Otani, J., Nankumo, T., Arita, K., Inamoto, S., Ariyoshi, M., & Shirakawa, M. (2009) · EMBO Reports · doi:10.1038/embor.2009.218 · Cited by 435 · cited 1×
“2011b) and the exclusion of de novo DNA methyltransferases by H3K4me3 methylation (Ooi et al. 2007; Otani et al. 2009; Guo et al. 2015; Noh et al. 2015).”
BackgroundLandscape Of Genetic Lesions In 944 Patients With Myelodysplastic Syndromes
Nagata, Y., Grossmann, V., Okuno, Y., Bacher, U., Nagae, G., Schnittger, S., Shiozawa, Y., Kon, A., Alpermann, T., Yoshida, K., et al. (2013) · Blood · doi:10.1182/blood.v122.21.521.521 · Cited by 430
Lorsbach, R. B., Moore, J., Mathew, S., Raimondi, S. C., Mukatira, S. T., & Downing, J. R. (2003) · Leukemia · doi:10.1038/sj.leu.2402834 · Cited by 416 · cited 1×
“The family of TET proteins was originally named due to the characterization of TET1 as a fusion partner in mixed-lineage leukemia (MLL)-rearranged AML (Ono et al. 2002; Lorsbach et al. 2003).”
BackgroundModulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX
Ko, M., An, J., Bandukwala, H. S., Chávez, L., Äijö, T., Pastor, W. A., Segal, M., Li, H., Koh, K. P., Lähdesmäki, H. J., et al. (2013) · Nature · doi:10.1038/nature12052 · Cited by 414
Minor, E. A., Court, B. L., Young, J. I., & Wang, G. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.c113.464800 · Cited by 413 · cited 1×
“In contrast, increasing the levels of vitamin C (ascorbic acid) has been shown to stimulate TET protein enzymatic activity in cultured cells as well as mouse tissues (Blaschke et al. 2013; Minor et al. 2013; Yin et al. 2013; Bachman et al. 2014).”
BackgroundEarly-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 392 · cited 1×
“In addition, TET activity plays an important role in induced pluripotent stem cell formation (Doege et al. 2012; Costa et al. 2013) as well as smooth muscle cell differentiation (Liu et al.”
BackgroundStructural insight into autoinhibition and histone H3-induced activation of DNMT3A
Guo, X., Wang, L., Li, J., Ding, Z., Xiao, J., Yin, X., He, S., Shi, P., Dong, L., Li, G., et al. (2015) · Nature · doi:10.1038/nature13899 · Cited by 361 · cited 1×
“2011b) and the exclusion of de novo DNA methyltransferases by H3K4me3 methylation (Ooi et al. 2007; Otani et al. 2009; Guo et al. 2015; Noh et al. 2015).”
BackgroundHon, 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 349
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 · cited 2×
“Finally, the successful generation and characterization of Tet1/ 2/3 triple-knockout ESCs have shown that combined TET activity is essential for supporting embryonic development (Dawlaty et al. 2014).”
BackgroundDeletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo
Abdel-Wahab, O. I., Gao, J., Adli, M., Dey, A., Trimarchi, T., Chung, Y. R., Kuscu, C., Hricik, T., Ndiaye‐Lobry, D., LaFave, L. M., et al. (2013) · The Journal of Experimental Medicine · doi:10.1084/jem.20131141 · Cited by 335
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 333
Self-citationIchiyama, K., Chen, T., Wang, X., Yan, X., Kim, B.-S., Tanaka, S., Ndiaye-Lobry, D., Deng, Y., Zou, Y., Zheng, P., et al. (2015) · Immunity · doi:10.1016/j.immuni.2015.03.005 · Cited by 327 · cited 1×
“Similarly, Tet2 deficiency induced in CD2 T cells is associated with aberrant cytokine production and leads to increased autoimmunity in a mouse model of human multiple sclerosis (Ichiyama et al. 2015).”
BackgroundAID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation
Nabel, C. S., Jia, H., Ye, Y., Shen, L., Goldschmidt, H. L., Stivers, J. T., Zhang, Y., & Kohli, R. M. (2012) · Nature Chemical Biology · doi:10.1038/nchembio.1042 · Cited by 326 · cited 1×
“Conversely, overexpression of TDG in HEK293 cells results in depletion of 5fC and 5caC with little or no change of 5mCand 5hmC (Nabel et al. 2012).”
BackgroundIurlaro, M., Ficz, G., Oxley, D., Raiber, E., Bachman, M., Booth, M. J., Andrews, S., Balasubramanian, S., & Reik, W. (2013) · Genome biology · doi:10.1186/gb-2013-14-10-r119 · Cited by 321 · cited 2×
“Instead, the much less abundant cytosine species 5fC and 5caC appear to interact with numerous proteins, including TDG, p53, DNA repair factors, chromatin remodeling factors, and forkhead box TFs (Iurlaro et al. 2013; Spruijt et al. 2013).”
BackgroundWT1 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 320
Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA
Zhang, L., Lu, X., Lu, J., Liang, H., Dai, Q., Xu, G., Luo, C., Jiang, H., & He, C. (2012) · Nature Chemical Biology · doi:10.1038/nchembio.914 · Cited by 314
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
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 301
Clonal architecture of chronic myelomonocytic leukemias
Itzykson, R., Kosmider, O., Renneville, A., Morabito, M., Preudhomme, C., Berthon, C., Adès, L., Fenaux, P., Platzbecker, U., Gagey, O., et al. (2013) · Blood · doi:10.1182/blood-2012-06-440347 · Cited by 291
Structural insight into substrate preference for TET-mediated oxidation
Hu, L., Lu, J., Cheng, J., Rao, Q., Li, Z., Hou, H., Lou, Z., Zhang, L., Li, W., Gong, W., et al. (2015) · Nature · doi:10.1038/nature15713 · Cited by 290 · cited 2×
“6-fold) substrates compared with the initial oxidation reaction of 5mC (Ito et al. 2011; Hu et al. 2015).”
BackgroundTen-Eleven Translocation-2 (TET2) Is a Master Regulator of Smooth Muscle Cell Plasticity
Liu, R., Yu, J. H., Tang, W. H., Qin, L., Zhang, X., Tellides, G., Hwa, J., Yu, J., & Martin, K. A. (2013) · Circulation · doi:10.1161/circulationaha.113.002887 · Cited by 289
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 285 · cited 1×
“Nonetheless, decreased expression of TET proteins and lower 5hmC levels are general hallmarks of many cancer types, including gastric, prostate, liver, lung, and breast cancer as well as glioblastoma and melanoma (Kudo et al. 2012; Lian et al. 2012; Turcan et al. 2012; Liu et al. 2013a; Yang et al. 2013).”
BackgroundRampal, R. K., Akalin, A., Madžo, J., Vasanthakumar, A., Pronier, E., Patel, J. L., Li, Y., Ahn, J., Abdel-Wahab, O. I., Shih, A. H., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.11.004 · Cited by 280
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 278 · cited 2×
“Genetic disruption of all three Tet proteins in mouse ESCs (Tet triple-knockout cells) is compatible with viability despite complete absence of 5hmCand a small but consistent increase in global DNA methylation level (Dawlaty et al. 2014; Lu et al. 2014).”
BackgroundOno, R., Taki, T., Taketani, T., Taniwaki, M., Kobayashi, H., & Hayashi, Y. (2002) · PubMed · Cited by 278
Landscape of TET2 mutations in acute myeloid leukemia
Weißmann, S., Alpermann, T., Grossmann, V., Kowarsch, A., Nadarajah, N., Eder, C., Dicker, F., Fasan, A., Haferlach, C., Haferlach, T., et al. (2011) · Leukemia · doi:10.1038/leu.2011.326 · Cited by 272 · cited 1×
“Follow-up studies in diverse patient groups quickly identified not just chromosomal aberrations but also frequent point mutations—including insertions, deletions, missense, nonsense, and frameshift mutations—that often result in truncations or decreased enzymatic activity of TET2 (Weissmann et al. 2012).”
BackgroundXu, 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
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
Self-citation5-Formylcytosine can be a stable DNA modification in mammals
Bachman, M., Uribe‐Lewis, S., Yang, X., Burgess, H. E., Iurlaro, M., Reik, W., Murrell, A., & Balasubramanian, S. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1848 · Cited by 269
TET proteins and the control of cytosine demethylation in cancer
Scourzic, L., Mouly, E., & Bernard, O. (2015) · Genome Medicine · doi:10.1186/s13073-015-0134-6 · Cited by 263 · cited 1×
“However, it should be noted that the types of mutations that accumulate in solid tumors are often missense mutations with unknown significance that may have relative little effect on TET activity (Scourzic et al. 2015).”
BackgroundTET1 is a tumor suppressor of hematopoietic malignancy
Cimmino, L., Dawlaty, M. M., Ndiaye‐Lobry, D., Yap, Y. S., Bakogianni, S., Yu, Y., Bhattacharyya, S., Shaknovich, R., Geng, H., Lobry, C., et al. (2015) · Nature Immunology · doi:10.1038/ni.3148 · Cited by 242 · cited 5×
“2012), whereas Tet1 deficiency leads to an overall lymphoid bias and dysregulated B-cell lineage differentiation (Cimmino et al. 2015).”
BackgroundInfluentialShih, A. H., Jiang, Y., Meydan, C., Shank, K., Pandey, S., Barreyro, L., Antony-Debre, I., Viale, A., Socci, N., Sun, Y., et al. (2015) · Cancer Cell · doi:10.1016/j.ccell.2015.03.009 · Cited by 236 · cited 1×
“AML1-ETO or FLT3-ITD (two common oncogenic alterations) in Tet2-depleted hematopoietic cells results in complete leukemogenic transformation into AML-like diseases (Rasmussen et al. 2015; Shih et al. 2015; Hatlen et al. 2016).”
BackgroundKellinger, M. W., Song, C., Chong, J. P. C., Lu, X., He, C., & Wang, D. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2346 · Cited by 235
Zhang, H., Zhang, X., Clark, E. A., Mulcahey, M., Huang, S. A., & Shi, Y. (2010) · Cell Research · doi:10.1038/cr.2010.156 · Cited by 221
Acute loss of TET function results in aggressive myeloid cancer in mice
An, J., González‐Avalos, E., Chawla, A., Jeong, M., López-Moyado, I. F., Li, W., Goodell, M. A., Chávez, L., Ko, M., & Rao, A. (2015) · Nature Communications · doi:10.1038/ncomms10071 · Cited by 215 · cited 2×
“In another study, the effects of combined Tet2 and Tet3 disruption (Tet2/3 double knockout) in the hematopoietic system were investigated (An et al. 2015).”
BackgroundPronier, E., Almire, C., Mokrani, H., Vasanthakumar, A., Simon, A., Monte-Mór, B. D. C. R., Massé, A., Couedic, J. P. L., Pendino, F., Carbonne, B., et al. (2011) · Blood · doi:10.1182/blood-2010-12-324707 · Cited by 204
TET proteins and 5‐methylcytosine oxidation in hematological cancers
Ko, M., An, J., Pastor, W. A., Koralov, S. B., Rajewsky, K., & Rao, A. (2014) · Immunological Reviews · doi:10.1111/imr.12239 · Cited by 202 · cited 1×
“Preliminary experiments using a hematopoietic-specific deletion of Tet3 failed to detect expansion of the HSC compartment or disrupted hematopoietic differentiation (Ko et al. 2015).”
BackgroundBraun, T., Itzykson, R., Renneville, A., Renzis, B. D., Dreyfus, F., Laribi, K., Bouabdallah, K. K., Vey, N., Toma, A., Récher, C., et al. (2011) · Blood · doi:10.1182/blood-2011-05-352039 · Cited by 201 · cited 1×
“Therapeutic intervention against this early aberration in AML, MDS, and CMML patients using demethylating agents (azacytidine and decitabine) have yielded inconclusive results (Braun et al. 2011; Itzykson et al. 2011; Bejar et al. 2014; Meldi et al. 2015).”
Recognition of 5-Hydroxymethylcytosine by the Uhrf1 SRA Domain
Frauer, C., Hoffmann, T., Bultmann, S., Casà, V., Cardoso, M. C., Antes, I., & Leonhardt, H. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021306 · Cited by 199 · cited 1×
“It has been shown that theDNMT1 interaction partnersUHRF1 and UHRF2 can bind 5hmC DNA (Frauer et al. 2011; Hashimoto et al. 2012; Iurlaro et al. 2013; Spruijt et al. 2013; Zhou et al. 2014).”
BackgroundDynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers
Sérandour, A. A., Avner, S., Oger, F., Bizot, M., Percevault, F., Lucchetti-Miganeh, C., Palierne, G., Gheeraert, C., Barloy-Hubler, F., Péron, C. L., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks595 · Cited by 199 · cited 1×
“There has been substantial interest inmapping cytosine oxidation products in the genome with the aim of understanding their role in gene regulation and DNA methylation dynamics (Pastor et al. 2011; Stroud et al. 2011; Szulwach et al. 2011; Williams et al. 2011; Wu et al. 2011a; Xu et al. 2011c; Sérandour et al. 2012).”
BackgroundConcurrent loss of Ezh2 and Tet2 cooperates in the pathogenesis of myelodysplastic disorders
Muto, T., Sashida, G., Oshima, M., Wendt, G. R., Mochizuki‐Kashio, M., Nagata, Y., Sanada, M., Miyagi, S., Saraya, A., Kamio, A., et al. (2013) · The Journal of Experimental Medicine · doi:10.1084/jem.20131144 · Cited by 191
Taberlay, P. C., Statham, A. L., Kelly, T. K., Clark, S. J., & Jones, P. A. (2014) · Genome Research · doi:10.1101/gr.163485.113 · Cited by 186 · cited 1×
“Increased DNA methylation is negatively correlated with chromatin accessibility and histone marks associated with enhancers (Hon et al. 2014; Taberlay et al. 2014; Rasmussen et al. 2015).”
BackgroundSpecific molecular signatures predict decitabine response in chronic myelomonocytic leukemia
Meldi, K. M., Qin, T., Buchi, F., Droin, N. M., Sotzen, J. R., Micol, J., Selimoglu‐Buet, D., Masala, E., Allione, B., Gioia, D. M., et al. (2015) · Journal of Clinical Investigation · doi:10.1172/jci78752 · Cited by 184 · cited 1×
“Therapeutic intervention against this early aberration in AML, MDS, and CMML patients using demethylating agents (azacytidine and decitabine) have yielded inconclusive results (Braun et al. 2011; Itzykson et al. 2011; Bejar et al. 2014; Meldi et al. 2015).”
Role of Tet1 and 5-hydroxymethylcytosine in cocaine action
Feng, J., Shao, N., Szulwach, K. E., Vialou, V., Huynh, J. L., Zhong, C., Le, T. T., Ferguson, D., Cahill, M. E., Li, Y., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.3976 · Cited by 181 · cited 1×
“For instance, loss of Tet activity is associated with altered neuronal activity and has been implicated in learning and memory processes as well as cocaine addiction (Hahn et al. 2013; Rudenko et al. 2013; Feng et al. 2015).”
BackgroundStructure of the MLL CXXC domain–DNA complex and its functional role in MLL-AF9 leukemia
Cierpicki, T., Risner, L. E., Grembecka, J. E., Lukasik, S. M., Popovic, R., Omonkowska, M., Shultis, D., Zeleznik‐Le, N. J., & Bushweller, J. H. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1714 · Cited by 179 · cited 1×
“Structural studies of CXXC domains in other proteins (Cierpicki et al. 2010; Song et al. 2011; Xu et al. 2011a) have shown that these can bind to a single CpG site.”
BackgroundNotch pathway activation targets AML-initiating cell homeostasis and differentiation
Lobry, C., Ntziachristos, P., Ndiaye‐Lobry, D., Oh, P., Cimmino, L., Zhu, N., Araldi, E., Hu, W., Freund, J. E., Abdel-Wahab, O. I., et al. (2013) · The Journal of Experimental Medicine · doi:10.1084/jem.20121484 · Cited by 169 · cited 1×
“In contrast, inactivation of the Notch pathway (Lobry et al. 2013) or expression of Rasmussen and Helin”
MethodMeta-analysis of IDH-mutant cancers identifies EBF1 as an interaction partner for TET2
Guilhamon, P., Eskandarpour, M., Halai, D., Wilson, G. A., Feber, A., Teschendorff, A. E., Gómez, V., Hergovich, A., Tirabosco, R., Amary, F. M., et al. (2013) · Nature Communications · doi:10.1038/ncomms3166 · Cited by 169 · cited 1×
“In fact, the TET2 protein, either endogenous or overexpressed, has been shown to bind tissuespecific TFs such as early B-cell factor 1 (EBF1) (Guilhamon et al. 2013) and WT1 (Rampal et al.”
BackgroundAn Extensive Network of TET2-Targeting MicroRNAs Regulates Malignant Hematopoiesis
Cheng, J., Guo, S., Chen, S., Mastriano, S., Liu, C., D’Alessio, A. C., Hysolli, E., Guo, Y., Yao, H., Megyola, C. M., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.08.050 · Cited by 164
Liu, C., Liu, L., Chen, X., Shen, J., Shan, J., Xu, Y., Yang, Z., Wu, L., Xia, F., Bie, P., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062828 · Cited by 161
Hill, P. W. S., Amouroux, R., & Hájková, P. (2014) · Genomics · doi:10.1016/j.ygeno.2014.08.012 · Cited by 161
Wu, H., Wu, X., Shen, L., & Zhang, Y. (2014) · Nature Biotechnology · doi:10.1038/nbt.3073 · Cited by 157 · cited 5×
“However, it should be noted that the overall distribution as well as enrichment of 5fC and 5caC in Tdg-depleted cells show that distal regulatory elements are the primary site of 5fC/5caC deposition (Wu et al. 2014).”
BackgroundInfluentialActive promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments
Jain, D., Baldi, S., Zabel, A., Straub, T., & Becker, P. B. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv637 · Cited by 156
miR-29 Represses the Activities of DNA Methyltransferases and DNA Demethylases
Morita, S., Horii, T., Kimura, M., Ochiya, T., Tajima, S., & Hatada, I. (2013) · International Journal of Molecular Sciences · doi:10.3390/ijms140714647 · Cited by 156 · cited 1×
“Moreover, several microRNAs, some of which are overexpressed in cancer, have been reported to directly target TET proteins (Cheng et al. 2013; Fu et al. 2013; Morita et al. 2013; Chuang et al. 2015).”
BackgroundMolecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex
Wang, L., Zhou, Y., Xu, L., Xiao, R., Lu, X., Chen, L., Chong, J. P. C., Li, H., He, C., Fu, X., et al. (2015) · Nature · doi:10.1038/nature14482 · Cited by 153
FBXL10 protects Polycomb-bound genes from hypermethylation
Boulard, M., Edwards, J. R., & Bestor, T. H. (2015) · Nature Genetics · doi:10.1038/ng.3272 · Cited by 153 · cited 1×
“In addition, transcriptionally repressed promoters and CpG islands (associated with PRC2 and marked by H3K27me3) also appear to be protected from ectopic DNA methylation by the polycomb-associated protein Fbxl10 (Boulard et al. 2015).”
BackgroundRole of DNMT3A, TET2, and IDH1/2 mutations in pre-leukemic stem cells in acute myeloid leukemia
Chan, S. M., & Majeti, R. (2013) · International Journal of Hematology · doi:10.1007/s12185-013-1407-8 · Cited by 142 · cited 1×
“First, TET2 mutations can be found in premalignant HSCs in MDS and AML patients and are preserved in the tumor bulk along with additional oncogenic mutations (Jan et al. 2012; Chan and Majeti 2013; Itzykson et al. 2013).”
BackgroundStructure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA
Hashimoto, H., Pais, J. E., Zhang, X., Saleh, L., Fu, Z.-Q., Dai, N., Junior, I. R. C., Zheng, Y., & Cheng, X. (2013) · Nature · doi:10.1038/nature12905 · Cited by 138 · cited 1×
“Structural studies suggest that this core catalytic region preferentially binds cytosines in a CpG context but does not interact with surrounding DNA bases and shows little or no specificity for flanking DNA sequences (Hu et al. 2013, 2015; Hashimoto et al. 2014b).”
BackgroundFu, X., Jin, L., Wang, X., Luo, A., Hu, J., Zheng, X., Tsark, W. M. K., Riggs, A. D., Ku, H. T., & Huang, W. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317397110 · Cited by 131 · cited 1×
“Moreover, several microRNAs, some of which are overexpressed in cancer, have been reported to directly target TET proteins (Cheng et al. 2013; Fu et al. 2013; Morita et al. 2013; Chuang et al. 2015).”
BackgroundThe structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain
Xu, C., Bian, C., Lam, R., Dong, A., & Min, J. (2011) · Nature Communications · doi:10.1038/ncomms1237 · Cited by 130 · cited 1×
“Structural studies of CXXC domains in other proteins (Cierpicki et al. 2010; Song et al. 2011; Xu et al. 2011a) have shown that these can bind to a single CpG site.”
BackgroundWilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequencePreprint
Hashimoto, H., Olanrewaju, Y. O., Zheng, Y., Wilson, G. G., Zhang, X., & Cheng, X. (2014) · Genes & Development · doi:10.1101/gad.250746.114 · Cited by 128 · cited 1×
“In addition, oxidation of cytosines in the DNA-binding motif of the TF Wilms tumor 1 (WT1; to 5hmC and 5fC but not 5caC) effectively disrupts protein–DNA interaction (Hashimoto et al. 2014a).”
BackgroundNeri, F., Incarnato, D., Křepelová, A., Rapelli, S., Anselmi, F., Parlato, C., Medana, C., Bello, F. D., & Oliviero, S. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.01.008 · Cited by 127 · cited 2×
“33 million modified sites with an average modification rate of 8%–10% (Neri et al. 2015).”
BackgroundKang, J., Lienhard, M., Pastor, W. A., Chawla, A., Novotny, M., Tsagaratou, A., Lasken, R. S., Thompson, E. C., Surani, M. A., Koralov, S. B., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1510510112 · Cited by 126 · cited 1×
“Constitutive deletion of Tet3 leads to neonatal lethality with 100% penetrance (Gu et al. 2011; Kang et al. 2015), whereas deletions of either Tet1 (Dawlaty et al.”
BackgroundEffects ofTET2mutations on DNA methylation in chronic myelomonocytic leukemia
Yamazaki, J., Taby, R. F., Vasanthakumar, A., Macrae, T. A., Ostler, K. R., Shen, L., Kantarjian, H. M., Estecio, M. R., Jelı́nek, J., Godley, L. A., et al. (2012) · Epigenetics · doi:10.4161/epi.7.2.19015 · Cited by 125
Alterations of metabolic genes and metabolites in cancer
Oermann, E. K., Wu, J., Guan, K., & Xiong, Y. (2012) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2012.01.013 · Cited by 125 · cited 1×
“Mutations in the genes coding for the metabolic enzymes isocitrate dehydrogenases 1 and 2 (IDH1/2), succinate dehydrogenase (SDH), and fumarate hydratase (FH) have been reported in a wide variety of liquid and solid tumors (Oermann et al. 2012).”
BackgroundCRL4 complex regulates mammalian oocyte survival and reprogramming by activation of TET proteins
Yu, C., Zhang, Y.-L., Pan, W.-W., Li, X.-M., Wang, Z.-W., Ge, Z.-J., Zhou, J.-J., Cang, Y., Tong, C., Sun, Q.-Y., et al. (2013) · Science · doi:10.1126/science.1244587 · Cited by 123
Interleukin 6 (IL‐6) and its receptor: Their role in plasma cell neoplasias
Hirano, T. (1991) · The International Journal Of Cell Cloning · doi:10.1002/stem.5530090303 · Cited by 123
Conceptual links between DNA methylation reprogramming in the early embryo and primordial germ cells
Seisenberger, S., Peat, J. R., & Reik, W. (2013) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2013.02.013 · Cited by 115 · cited 1×
“For instance, DNMT1 is excluded from the nucleus in early embryos (Seisenberger et al. 2013), and the rate of demethylation of both paternal and maternal genomes cannot be explained by a passive demethylation pathway (both TET-dependent and TET-independent) alone (Wang et al.”
BackgroundChen, E., Schneider, R. K., Breyfogle, L. J., Rosen, E. A., Poveromo, L., Elf, S., Ko, A., Brumme, K. M., Levine, R. L., Ebert, B. L., et al. (2014) · Blood · doi:10.1182/blood-2014-04-567024 · Cited by 115 · cited 1×
“The combination of Tet2 disruption with either Asxl1, Ezh2, or Jak2 mutant alleles results in MDS and MPN-like disease phenotypes (AbdelWahab et al. 2013; Muto et al. 2013; Chen et al. 2015; Kameda et al. 2015), whereas expression of hyperactive KIT leads to systemic mastocytosis (Soucie et al.”
BackgroundCRL4VprBP E3 Ligase Promotes Monoubiquitylation and Chromatin Binding of TET Dioxygenases
Nakagawa, T., Lv, L., Nakagawa, M., Yu, Y., Yu, C. Y., D’Alessio, A. C., Nakayama, K., Fan, H., Chen, X., & Xiong, Y. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.12.002 · Cited by 114 · cited 2×
“Interestingly, several TET2 missense mutations observed in AML patients affect K1299 or the surrounding region (Nakagawa et al. 2015).”
BackgroundPutiri, E. L., Tiedemann, R. L., Thompson, J. J., Liu, C., Ho, T. H., Choi, J.-H., & Robertson, K. D. (2014) · Genome biology · doi:10.1186/gb-2014-15-6-r81 · Cited by 111 · cited 1×
“In agreement with the fact that the CXXC domain interacts with only one CpG, Tet1 has been shown to be associated with distal regulatory elements as well as genome-wide diffuse 5hmC deposition (Stadler et al. 2011; Putiri et al. 2014), and Tet3mediated cytosine oxidation in the developing embryo occurs at a wide range…”
BackgroundIn aggressive forms of mastocytosis, TET2 loss cooperates with c-KITD816V to transform mast cells
Soucie, E. L., Hanssens, K., Mercher, T., Georgin‐Lavialle, S., Damaj, G. L., Livideanu, C. B., Chandesris, M., Acin, Y., Letard, S., Sepulveda, P. D., et al. (2012) · Blood · doi:10.1182/blood-2011-12-397588 · Cited by 108 · cited 1×
“2015), whereas expression of hyperactive KIT leads to systemic mastocytosis (Soucie et al. 2012; De Vita et al. 2014).”
BackgroundStructural Basis for Hydroxymethylcytosine Recognition by the SRA Domain of UHRF2
Zhou, T., Xiong, J., Wang, M., Yang, N., Wong, J., Zhu, B., & Xu, R.-M. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.04.003 · Cited by 106
Combined Loss of Tet1 and Tet2 Promotes B Cell, but Not Myeloid Malignancies, in Mice
Zhao, Z., Chen, L., Dawlaty, M. M., Pan, F., Weeks, O. I., Zhou, Y., Cao, Z., Shi, H., Wang, J., Lin, L., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.10.037 · Cited by 104 · cited 2×
“2015) as well as combined Tet1 and Tet2 deficiency (Tet1/2 double knockout) (Zhao et al. 2015) are prone to developing late-onset B-cell lymphoma.”
BackgroundChuang, K., Whitney‐Miller, C. L., Chu, C., Zhou, Z., Dokus, M. K., Schmit, S., & Barry, C. T. (2015) · Hepatology · doi:10.1002/hep.27816 · Cited by 100 · cited 1×
“Moreover, several microRNAs, some of which are overexpressed in cancer, have been reported to directly target TET proteins (Cheng et al. 2013; Fu et al. 2013; Morita et al. 2013; Chuang et al. 2015).”
BackgroundNoh, K., Wang, H., Kim, H. R., Wenderski, W., Fang, F., Li, C. H., Dewell, S. B., Hughes, S. H., Melnick, A. M., Patel, D. J., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.05.017 · Cited by 93
Yamazaki, J., Jelı́nek, J., Lu, Y., Cesaroni, M., Madžo, J., Neumann, F., He, R. L., Taby, R. F., Vasanthakumar, A., Macrae, T. A., et al. (2015) · Cancer Research · doi:10.1158/0008-5472.can-14-0739 · Cited by 90 · cited 1×
“In contrast, they did not detect changes in DNAmethylation at CpG islands (Yamazaki et al. 2015).”
BackgroundTET2 is essential for survival and hematopoietic stem cell homeostasis
Shide, K., Kameda, T., Shimoda, H. K., Yamaji, T., Abe, H., Kamiunten, A., Sekine, M., Hidaka, T., Katayose, K., Kubuki, Y., et al. (2012) · Leukemia · doi:10.1038/leu.2012.94 · Cited by 90 · cited 1×
“Loss of Tet2 results in age-associated extramedullary hematopoiesis and expansion of monocytes and granulocytes in the spleen (Ko et al. 2011; Li et al. 2011; Moran-Crusio et al. 2011; Quivoron et al. 2011; Shide et al. 2012), whereas Tet1 deficiency leads to an overall lymphoid bias and dysregulated B-cell lineage di…”
BackgroundKameda, T., Shide, K., Yamaji, T., Kamiunten, A., Sekine, M., Taniguchi, Y., Hidaka, T., Kubuki, Y., Shimoda, H. K., Marutsuka, K., et al. (2014) · Blood · doi:10.1182/blood-2014-04-555508 · Cited by 87
Pérez, C., Martínez‐Calle, N., Martín-Subero, J. I., Segura, V., Delabesse, É., Fernández‐Mercado, M., Gárate, L., Álvarez, S., Rifón, J., Varea, S., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0031605 · Cited by 78 · cited 1×
“2012) or predominantly DNA-hypomethylated (Ko et al. 2010; Pérez et al. 2012), whereas others reported increased levels of DNA methylation (Figueroa et al.”
BackgroundCharting oxidized methylcytosines at base resolution
Wu, H., & Zhang, Y. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3071 · Cited by 76
Ji, D., Lin, K., Song, J., & Wang, Y. (2014) · Molecular BioSystems · doi:10.1039/c4mb00150h · Cited by 60 · cited 2×
“2003; Jones and Liang 2009), and these enzymes readily methylate a DNA substrate containing 5hmC (Hashimoto et al. 2012; Ji et al. 2014).”
Knappskog, S., Myklebust, L. M., Busch, C., Aloysius, T. A., Varhaug, J. E., Lønning, P. E., Lillehaug, J. R., & Pendino, F. (2011) · Annals of Oncology · doi:10.1093/annonc/mdq737 · Cited by 46 · cited 1×
“The TET2-interacting proteins IDAX/CXXC4 and RINF/CXXC5 are overexpressed in several solid tumors, including breast and colorectal cancer (Knappskog et al. 2011), and are reported to have a negative impact on the stability and function of TET2 (Ko et al.”
BackgroundVita, S. D., Schneider, R. K., Garcia, M., Wood, J. A., Gavillet, M., Ebert, B. L., Gerbaulet, A., Roers, A., Levine, R. L., Mullally, A., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0096209 · Cited by 38
Ittel, A., Jeandidier, É., Hélias, C., Perrusson, N., Humbrecht, C., Lioure, B., Mazurier, I., Mayeur‐Rousse, C., Lavaux, A., Thiebault, S., et al. (2013) · Haematologica · doi:10.3324/haematol.2013.096750 · Cited by 35
Hashimoto, H., Pais, J. E., Dai, N., Junior, I. R. C., Zhang, X., Zheng, Y., & Cheng, X. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv870 · Cited by 33 · cited 1×
“Interestingly, a recent report identified mutants of the TET1 protein in the amoeba Naegleria that primarily generate 5hmC with little or no further oxidation to 5fC and 5caC (Hashimoto et al. 2015).”
BackgroundIntegrative genetic analysis of mouse and human AML identifies cooperating disease alleles
Hatlen, M. A., Arora, K. S., Vacic, V., Grabowska, E. A., Liao, W., Riley-Gillis, B. M., Oschwald, D. M., Wang, L., Joergens, J. E., Shih, A. H., et al. (2015) · The Journal of Experimental Medicine · doi:10.1084/jem.20150524 · Cited by 28
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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
The DNA methyltransferase family: a versatile toolkit for epigenetic regulation
Lyko, F. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.80 · Cited by 1,510
Protein O-GlcNAcylation: emerging mechanisms and functions
Yang, X., & Qian, K. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.22 · Cited by 1,222
Restoration of TET2 Function Blocks Aberrant Self-Renewal and Leukemia Progression
Cimmino, L., Dolgalev, I., Wang, Y., Yoshimi, A., Martin, G. H., Wang, J., Ng, V., Xia, B., Witkowski, M. T., Mitchell-Flack, M., et al. (2017) · Cell · doi:10.1016/j.cell.2017.07.032 · Cited by 707
DNA Methylation Clocks in Aging: Categories, Causes, and Consequences
Field, A. E., Robertson, N., Wang, T., Havas, A. P., Ideker, T., & Adams, P. D. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.08.008 · Cited by 644
Metadata
- Authors
- Rasmussen, K. D., & Helin, K.
- Affiliations
- University of Copenhagen (DK)
- Corresponding author
- Helin, Kristian
- Venue
- Genes & Development
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2016-04-01
- Volume
- 30
- Issue
- 7
- Pages
- 733-750
- ISSN
- 0890-9369 (ISSN-L)
- 1549-5477
- PMC
- PMC4826392
- OpenAlex
- W2325267338
- Cited by
- 1,040
- References
- 162
- Citations by year
- 2026: 56 · 2025: 87 · 2024: 116 · 2023: 100 · 2022: 135 · 2021: 141 · 2020: 131 · 2019: 97 · 2018: 83 · 2017: 60 · 2016: 30
- Type
- posted content
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Genes & Development (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by-nc)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Danish Medical Research Council (1333-00120B)
- European Research Council (294666_DNAMET)
- Danish Cancer Society
- Danish National Research Foundation (DNRF 82)
- Danish Council for Strategic Research
- Novo Nordisk Foundation
- 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 › Molecular Biology › Cancer-related gene regulation
- Keywords
- TET enzymes, DNA methylation, 5-methylcytosine oxidation, TET2, demethylation, cancer, developmental regulation, transcriptional regulation, gene expression
- MeSH terms
- Animals, Cytosine, DNA-Binding Proteins, Humans, Neoplasms, Oxidation-Reduction, Proto-Oncogene Proteins, Gene Expression Regulation, Neoplastic, DNA Methylation, Epigenesis, Genetic, Dioxygenases
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