201
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Lee M, Zhou Y, Huang Y. An Engineered Split-TET2 Enzyme for Chemical-inducible DNA Hydroxymethylation and Epigenetic Remodeling. J Vis Exp 2017. [PMID: 29286410 DOI: 10.3791/56858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
DNA methylation is a stable and heritable epigenetic modification in the mammalian genome and is involved in regulating gene expression to control cellular functions. The reversal of DNA methylation, or DNA demethylation, is mediated by the ten-eleven translocation (TET) protein family of dioxygenases. Although it has been widely reported that aberrant DNA methylation and demethylation are associated with developmental defects and cancer, how these epigenetic changes directly contribute to the subsequent alteration in gene expression or disease progression remains unclear, largely owing to the lack of reliable tools to accurately add or remove DNA modifications in the genome at defined temporal and spatial resolution. To overcome this hurdle, we designed a split-TET2 enzyme to enable temporal control of 5-methylcytosine (5mC) oxidation and subsequent remodeling of epigenetic states in mammalian cells by simply adding chemicals. Here, we describe methods for introducing a chemical-inducible epigenome remodeling tool (CiDER), based on an engineered split-TET2 enzyme, into mammalian cells and quantifying the chemical inducible production of 5-hydroxymethylcytosine (5hmC) with immunostaining, flow cytometry or a dot-blot assay. This chemical-inducible epigenome remodeling tool will find broad use in interrogating cellular systems without altering the genetic code, as well as in probing the epigenotype-phenotype relations in various biological systems.
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Affiliation(s)
- Minjung Lee
- Centre for Epigenetics and Disease Prevention, Department of Molecular and Cellular Medicine, Institute of Biosciences and Technology, College of Medicine, Texas A&M University
| | - Yubin Zhou
- Centre for Translational Cancer Research, Department of Medical Physiology, Institute of Biosciences and Technology, College of Medicine, Texas A&M University;
| | - Yun Huang
- Centre for Epigenetics and Disease Prevention, Department of Molecular and Cellular Medicine, Institute of Biosciences and Technology, College of Medicine, Texas A&M University;
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202
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Zhao M, Li MY, Gao XF, Jia SJ, Gao KQ, Zhou Y, Zhang HH, Huang Y, Wang J, Wu HJ, Lu QJ. Downregulation of BDH2 modulates iron homeostasis and promotes DNA demethylation in CD4 + T cells of systemic lupus erythematosus. Clin Immunol 2017; 187:113-121. [PMID: 29113828 DOI: 10.1016/j.clim.2017.11.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 12/31/2022]
Abstract
DNA hypomethylation plays an important role in the pathogenesis of systemic lupus erythematosus (SLE). Here we investigated whether 3-hydroxy butyrate dehydrogenase 2 (BDH2), a modulator of intracellular iron homeostasis, was involved in regulating DNA hypomethylation and hyper-hydroxymethylation in lupus CD4+ T cells. Our results showed that BDH2 expression was decreased, intracellular iron was increased, global DNA hydroxymethylation level was elevated, while methylation level was reduced in lupus CD4+ T cells compared with healthy controls. The decreased BDH2 contributed to DNA hyper-hydroxymethylation and hypomethylation via increasing intracellular iron in CD4+ T cells, which led to overexpression of immune related genes. Moreover, we showed that BDH2 was the target gene of miR-21. miR-21 promoted DNA demethylation in CD4+ T cells through inhibiting BDH2 expression. Our data demonstrated that the dysregulation of iron homeostasis in CD4+ T cells induced by BDH2 deficiency contributes to DNA demethylation and self-reactive T cells in SLE.
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Affiliation(s)
- Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China.
| | - Meng-Ying Li
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Xiao-Fei Gao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Su-Jie Jia
- Department of Pharmaceutics, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Ke-Qin Gao
- Department of Pharmaceutics, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Yin Zhou
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Hui-Hui Zhang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Yi Huang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Jing Wang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Hai-Jing Wu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Qian-Jin Lu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China.
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203
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The sequence preference of DNA methylation variation in mammalians. PLoS One 2017; 12:e0186559. [PMID: 29045493 PMCID: PMC5646869 DOI: 10.1371/journal.pone.0186559] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/03/2017] [Indexed: 11/19/2022] Open
Abstract
Methylation of cytosine at the 5 position of the pyrimidine ring is the most prevalent and significant epigenetic modifications in mammalian DNA. The CpG methylation level shows a bimodal distribution but the bimodality can be overestimated due to the heterogeneity of per-base depth. Here, we developed an algorithm to eliminate the effect of per-base depth inhomogeneity on the bimodality and obtained a random CpG methylation distribution. By quantifying the deviation of the observed methylation distribution and the random one using the information formula, we find that in tetranucleotides 5’-N5CGN3-3’ (N5, N3 = A, C, G or T), GCGN3 and CCGN3 show less apparent deviation than ACGN3 and TCGN3, indicating that GCGN3 and CCGN3 are less variant in their level of methylation. The methylation variation of N5CGN3 are conserved among different cells, tissues and species, implying common features in the mechanisms of methylation and demethylation, presumably mediated by DNMTs and TETs in mammalians, respectively. Sequence dependence of DNA methylation variation also relates to gene regulatory and promotes the reexamination of the role of DNA sequence in fundamental biological processes.
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204
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Acetylation Enhances TET2 Function in Protecting against Abnormal DNA Methylation during Oxidative Stress. Mol Cell 2017; 65:323-335. [PMID: 28107650 DOI: 10.1016/j.molcel.2016.12.013] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 08/09/2016] [Accepted: 12/15/2016] [Indexed: 11/24/2022]
Abstract
TET proteins, by converting 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), are hypothesized, but not directly shown, to protect promoter CpG islands (CGIs) against abnormal DNA methylation (DNAm) in cancer. We define such a protective role linked to DNA damage from oxidative stress (OS) known to induce this abnormality. TET2 removes aberrant DNAm during OS through interacting with DNA methyltransferases (DNMTs) in a "Yin-Yang" complex targeted to chromatin and enhanced by p300 mediated TET2 acetylation. Abnormal gains of DNAm and 5hmC occur simultaneously in OS, and knocking down TET2 dynamically alters this balance by enhancing 5mC and reducing 5hmC. TET2 reduction results in hypermethylation of promoter CGIs and enhancers in loci largely overlapping with those induced by OS. Thus, TET2 indeed may protect against abnormal, cancer DNAm in a manner linked to DNA damage.
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205
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Martinez S, Fellner M, Herr CQ, Ritchie A, Hu J, Hausinger RP. Structures and Mechanisms of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme: Substrate Binding Creates a Twist. J Am Chem Soc 2017; 139:11980-11988. [PMID: 28780854 PMCID: PMC5599930 DOI: 10.1021/jacs.7b06186] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The ethylene-forming enzyme (EFE) from Pseudomonas syringae pv. phaseolicola PK2 is a member of the mononuclear nonheme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenase superfamily. EFE converts 2OG into ethylene plus three CO2 molecules while also catalyzing the C5 hydroxylation of l-arginine (l-Arg) driven by the oxidative decarboxylation of 2OG to form succinate and CO2. Here we report 11 X-ray crystal structures of EFE that provide insight into the mechanisms of these two reactions. Binding of 2OG in the absence of l-Arg resulted in predominantly monodentate metal coordination, distinct from the typical bidentate metal-binding species observed in other family members. Subsequent addition of l-Arg resulted in compression of the active site, a conformational change of the carboxylate side chain metal ligand to allow for hydrogen bonding with the substrate, and creation of a twisted peptide bond involving this carboxylate and the following tyrosine residue. A reconfiguration of 2OG achieves bidentate metal coordination. The dioxygen binding site is located on the metal face opposite to that facing l-Arg, thus requiring reorientation of the generated ferryl species to catalyze l-Arg hydroxylation. Notably, a phenylalanyl side chain pointing toward the metal may hinder such a ferryl flip and promote ethylene formation. Extensive site-directed mutagenesis studies supported the importance of this phenylalanine and confirmed the essential residues used for substrate binding and catalysis. The structural and functional characterization described here suggests that conversion of 2OG to ethylene, atypical among Fe(II)/2OG oxygenases, is facilitated by the binding of l-Arg which leads to an altered positioning of the carboxylate metal ligand, a resulting twisted peptide bond, and the off-line geometry for dioxygen coordination.
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Affiliation(s)
- Salette Martinez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Matthias Fellner
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Caitlyn Q Herr
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Anastasia Ritchie
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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206
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Zhang P, Hastert FD, Ludwig AK, Breitwieser K, Hofstätter M, Cardoso MC. DNA base flipping analytical pipeline. Biol Methods Protoc 2017; 2:bpx010. [PMID: 32161792 PMCID: PMC6994035 DOI: 10.1093/biomethods/bpx010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 06/01/2017] [Accepted: 06/07/2017] [Indexed: 11/20/2022] Open
Abstract
DNA base modifications and mutations are observed in all genomes throughout the kingdoms of life. Proteins involved in their establishment and removal were shown to use a base flipping mechanism to access their substrates. To better understand how proteins flip DNA bases to modify or remove them, we optimized and developed a pipeline of methods to step-by-step detect the process starting with protein–DNA interaction, base flipping itself and the ensuing DNA base modification or excision. As methylcytosine is the best-studied DNA modification, here we focus on the process of writing, modifying and reading this DNA base. Using multicolor electrophoretic mobility shift assays, we show that the methylcytosine modifier Tet1 exhibits little DNA sequence specificity with only a slight preference for methylated CpG containing DNA. A combination of chloroacetaldehyde treatment and high-resolution melting temperature analysis allowed us to detect base flipping induced by the methylcytosine modifier Tet1 as well as the methylcytosine writer M.HpaII. Finally, we show that high-resolution melting temperature analysis can be used to detect the activity of glycosylases, methyltransferases and dioxigenases on DNA substrates. Taken together, this DNA base flipping analytical pipeline (BaFAP) provide a complete toolbox for the fast and sensitive analysis of proteins that bind, flip and modify or excise DNA bases.
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Affiliation(s)
- Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Germany
| | - Florian D Hastert
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Germany
| | - Anne K Ludwig
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Germany
| | - Kai Breitwieser
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Germany
| | | | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Germany
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207
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Ludwig AK, Zhang P, Hastert FD, Meyer S, Rausch C, Herce HD, Müller U, Lehmkuhl A, Hellmann I, Trummer C, Storm C, Leonhardt H, Cardoso MC. Binding of MBD proteins to DNA blocks Tet1 function thereby modulating transcriptional noise. Nucleic Acids Res 2017; 45:2438-2457. [PMID: 27923996 PMCID: PMC5389475 DOI: 10.1093/nar/gkw1197] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/20/2016] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is a hallmark of various human disorders, indicating that the spatial and temporal regulation of methylation readers and modifiers is imperative for development and differentiation. In particular, the cross-regulation between 5-methylcytosine binders (MBD) and modifiers (Tet) has not been investigated. Here, we show that binding of Mecp2 and Mbd2 to DNA protects 5-methylcytosine from Tet1-mediated oxidation. The mechanism is not based on competition for 5-methylcytosine binding but on Mecp2 and Mbd2 directly restricting Tet1 access to DNA. We demonstrate that the efficiency of this process depends on the number of bound MBDs per DNA molecule. Accordingly, we find 5-hydroxymethylcytosine enriched at heterochromatin of Mecp2-deficient neurons of a mouse model for Rett syndrome and Tet1-induced reexpression of silenced major satellite repeats. These data unveil fundamental regulatory mechanisms of Tet enzymes and their potential pathophysiological role in Rett syndrome. Importantly, it suggests that Mecp2 and Mbd2 have an essential physiological role as guardians of the epigenome.
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Affiliation(s)
- Anne K Ludwig
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Florian D Hastert
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Stephanie Meyer
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Henry D Herce
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Udo Müller
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Carina Trummer
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Christian Storm
- Chemical Plant Ecology, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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208
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Bowman RL, Levine RL. TET2 in Normal and Malignant Hematopoiesis. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026518. [PMID: 28242787 DOI: 10.1101/cshperspect.a026518] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ten-eleven translocation (TET) family of enzymes were originally cloned from the translocation breakpoint of t(10;11) in infant acute myeloid leukemia (AML) with subsequent genomic analyses revealing somatic mutations and suppressed expression of TET family members across a range of malignancies, particularly enriched in hematological neoplasms. The TET family of enzymes is responsible for the hydroxylation of 5-methylcytosines (5-mC) to 5-hydroxymethylcytosine (5-hmC), followed by active and passive mechanisms leading to DNA demethylation. Given the complexity and importance of DNA methylation events in cellular proliferation and differentiation, it comes as no surprise that the TET family of enzymes is intricately regulated by both small molecules and regulatory cooperating proteins. Here, we review the structure and function of TET2, its interactions with cooperating mutations and small molecules, and its role in aberrant hematopoiesis.
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Affiliation(s)
- Robert L Bowman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021
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209
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Zhang P, Rausch C, Hastert FD, Boneva B, Filatova A, Patil SJ, Nuber UA, Gao Y, Zhao X, Cardoso MC. Methyl-CpG binding domain protein 1 regulates localization and activity of Tet1 in a CXXC3 domain-dependent manner. Nucleic Acids Res 2017; 45:7118-7136. [PMID: 28449087 PMCID: PMC5499542 DOI: 10.1093/nar/gkx281] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 03/30/2017] [Accepted: 04/06/2017] [Indexed: 12/20/2022] Open
Abstract
Cytosine modifications diversify and structure the genome thereby controlling proper development and differentiation. Here, we focus on the interplay of the 5-methylcytosine reader Mbd1 and modifier Tet1 by analyzing their dynamic subcellular localization and the formation of the Tet oxidation product 5-hydroxymethylcytosine in mammalian cells. Our results demonstrate that Mbd1 enhances Tet1-mediated 5-methylcytosine oxidation. We show that this is due to enhancing the localization of Tet1, but not of Tet2 and Tet3 at heterochromatic DNA. We find that the recruitment of Tet1 and concomitantly its catalytic activity eventually leads to the displacement of Mbd1 from methylated DNA. Finally, we demonstrate that increased Tet1 heterochromatin localization and 5-methylcytosine oxidation are dependent on the CXXC3 domain of Mbd1, which recognizes unmethylated CpG dinucleotides. The Mbd1 CXXC3 domain deletion isoform, which retains only binding to methylated CpGs, on the other hand, blocks Tet1-mediated 5-methylcytosine to 5-hydroxymethylcytosine conversion, indicating opposite biological effects of Mbd1 isoforms. Our study provides new insights on how cytosine modifications, their modifiers and readers cross-regulate themselves.
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Affiliation(s)
- Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Florian D. Hastert
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Boyana Boneva
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Alina Filatova
- Stem Cell and Developmental Biology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sujit J. Patil
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Ulrike A. Nuber
- Stem Cell and Developmental Biology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Yu Gao
- Waisman Center & Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Xinyu Zhao
- Waisman Center & Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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210
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Yin X, Xu Y. Structure and Function of TET Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 945:275-302. [PMID: 27826843 DOI: 10.1007/978-3-319-43624-1_12] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mammalian DNA methylation mainly occurs at the carbon-C5 position of cytosine (5mC). TET enzymes were discovered to successively oxidize 5mC to 5-hydromethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). TET enzymes and oxidized 5mC derivatives play important roles in various biological and pathological processes, including regulation of DNA demethylation, gene transcription, embryonic development, and oncogenesis. In this chapter, we will discuss the discovery of TET-mediated 5mC oxidation and the structure, function, and regulation of TET enzymes.
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Affiliation(s)
- Xiaotong Yin
- Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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211
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Sudhamalla B, Dey D, Breski M, Islam K. A rapid mass spectrometric method for the measurement of catalytic activity of ten-eleven translocation enzymes. Anal Biochem 2017. [PMID: 28647531 DOI: 10.1016/j.ab.2017.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymatic methylation at carbon five on cytosine (5mC) in DNA is a hallmark of mammalian epigenetic programming and is critical to gene regulation during early embryonic development. It has recently been shown that dynamic erasure of 5mC by three members of the ten-eleven translocation (TET) family plays a key role in cellular differentiation. TET enzymes belong to Fe (II)- and 2-ketoglutarate (2KG) dependent dioxygenases that successively oxidize 5mC to 5-hydroxymethyl cytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5CaC), thus providing a chemical basis for the removal of 5mC which once was thought to be a permanent mark in mammalian genome. Since then a wide range of biochemical assays have been developed to characterize TET activity. Majority of these methods require multi-step processing to detect and quantify the TET-mediated oxidized products. In this study, we have developed a MALDI mass spectrometry based method that directly measures the TET activity with high sensitivity while eliminating the need for any intermediate processing steps. We applied this method to the measurement of enzymatic activity of TET2 and 3, Michaleis-Menten parameters (KM and kcat) of TET-2KG pairs and inhibitory concentration (IC50) of known small-molecule inhibitors of TETs. We further demonstrated the suitability of the assay to analyze chemoenzymatic labeling of 5hmC by β-glucosyltransferase, highlighting the potential for broad application of our method in deconvoluting the functions of novel DNA demethylases.
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Affiliation(s)
- Babu Sudhamalla
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Debasis Dey
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Megan Breski
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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212
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Yin R, Mo J, Dai J, Wang H. Nickel(II) Inhibits Tet-Mediated 5-Methylcytosine Oxidation by High Affinity Displacement of the Cofactor Iron(II). ACS Chem Biol 2017; 12:1494-1498. [PMID: 28467834 DOI: 10.1021/acschembio.7b00261] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ten-eleven translocation (Tet) family proteins are Fe(II)- and 2-oxoglutarate-dependent dioxygenases that regulate the dynamics of DNA methylation by catalyzing the oxidation of DNA 5-methylcytosine (5mC). To exert physiologically important functions, redox-active iron chelated in the catalytic center of Tet proteins directly involves the oxidation of the multiple substrates. To understand the function and interaction network of Tet dioxygenases, it is interesting to obtain high affinity and a specific inhibitor. Surprisingly, here we found that natural Ni(II) ion can bind to the Fe(II)-chelating motif (HXD) with an affinity of 7.5-fold as high as Fe(II). Consistently, we further found that Ni(II) ion can displace the cofactor Fe(II) of Tet dioxygenases and inhibit Tet-mediated 5mC oxidation activity with an estimated IC50 of 1.2 μM. Essentially, Ni(II) can be used as a high affinity and selective inhibitor to explore the function and dynamics of Tet proteins.
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Affiliation(s)
- Ruichuan Yin
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiezhen Mo
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiayin Dai
- Key
Laboratory of Animal Ecology and Conservation Biology, Institute of
Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hailin Wang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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213
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Yamagata K, Kobayashi A. The cysteine-rich domain of TET2 binds preferentially to mono- and dimethylated histone H3K36. J Biochem 2017; 161:327-330. [PMID: 28130413 PMCID: PMC5412023 DOI: 10.1093/jb/mvx004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 01/19/2017] [Indexed: 11/14/2022] Open
Abstract
Missense mutations in Ten-eleven translocation 2 (TET2) gene are frequently found in leukaemia patients. Although mutations span the entire coding region, they tend to cluster in the C-terminal enzymatic domain and a cysteine-rich (CR) domain of unknown function. Herein, we found the CR domain binds chromatin preferentially at the histone H3 tail by recognising H3 lysine 36 mono- and dimethylation (H3K36me1/2). Importantly, missense mutations in the CR domain perturbed TET2 recruitment to the target locus and its enzymatic activities. Our findings identify a novel H3K36me recognition domain and uncover a critical link between histone modification and DNA hydroxylation in leukaemogenesis.
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Affiliation(s)
- Kazuyuki Yamagata
- Division of Newborn Medicine, Children's Hospital Boston.,Department of Cell Biology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.,Organization for Research Initiatives and Development, Doshisha University
| | - Akira Kobayashi
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe 610-0394, Japan
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214
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Abstract
In mammals, DNA methylation in the form of 5-methylcytosine (5mC) can be actively reversed to unmodified cytosine (C) through TET dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), followed by replication-dependent dilution or thymine DNA glycosylase (TDG)-dependent base excision repair. In the past few years, biochemical and structural studies have revealed mechanistic insights into how TET and TDG mediate active DNA demethylation. Additionally, many regulatory mechanisms of this process have been identified. Technological advances in mapping and tracing the oxidized forms of 5mC allow further dissection of their functions. Furthermore, the biological functions of active DNA demethylation in various biological contexts have also been revealed. In this Review, we summarize the recent advances and highlight key unanswered questions.
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215
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5-Formylcytosine does not change the global structure of DNA. Nat Struct Mol Biol 2017; 24:544-552. [PMID: 28504696 DOI: 10.1038/nsmb.3411] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/13/2017] [Indexed: 01/14/2023]
Abstract
The mechanism by which the recently identified DNA modification 5-formylcytosine (fC) is recognized by epigenetic writer and reader proteins is not known. Recently, an unusual DNA structure, F-DNA, has been proposed as the basis for enzyme recognition of clusters of fC. We used NMR and X-ray crystallography to compare several modified DNA duplexes with unmodified analogs and found that in the crystal state the duplexes all belong to the A family, whereas in solution they are all members of the B family. We found that, contrary to previous findings, fC does not significantly affect the structure of DNA, although there are modest local differences at the modification sites. Hence, global conformation changes are unlikely to account for the recognition of this modified base, and our structural data favor a mechanism that operates at base-pair resolution for the recognition of fC by epigenome-modifying enzymes.
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216
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An J, Rao A, Ko M. TET family dioxygenases and DNA demethylation in stem cells and cancers. Exp Mol Med 2017; 49:e323. [PMID: 28450733 PMCID: PMC6130217 DOI: 10.1038/emm.2017.5] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 12/15/2022] Open
Abstract
The methylation of cytosine and subsequent oxidation constitutes a fundamental epigenetic modification in mammalian genomes, and its abnormalities are intimately coupled to various pathogenic processes including cancer development. Enzymes of the Ten–eleven translocation (TET) family catalyze the stepwise oxidation of 5-methylcytosine in DNA to 5-hydroxymethylcytosine and further oxidation products. These oxidized 5-methylcytosine derivatives represent intermediates in the reversal of cytosine methylation, and also serve as stable epigenetic modifications that exert distinctive regulatory roles. It is becoming increasingly obvious that TET proteins and their catalytic products are key regulators of embryonic development, stem cell functions and lineage specification. Over the past several years, the function of TET proteins as a barrier between normal and malignant states has been extensively investigated. Dysregulation of TET protein expression or function is commonly observed in a wide range of cancers. Notably, TET loss-of-function is causally related to the onset and progression of hematologic malignancy in vivo. In this review, we focus on recent advances in the mechanistic understanding of DNA methylation–demethylation dynamics, and their potential regulatory functions in cellular differentiation and oncogenic transformation.
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Affiliation(s)
- Jungeun An
- Department of Biological Sciences, Chonbuk National University, Jeonju, Korea
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA.,Department of Pharmacology and Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Myunggon Ko
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, Korea.,School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
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217
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Wang JC, Zhu Y, Wu L, Dong E. Progress in Pharmacological Sciences in China. Mol Pharmacol 2017; 92:188-192. [PMID: 28404616 DOI: 10.1124/mol.116.108167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/04/2017] [Indexed: 11/22/2022] Open
Abstract
Pharmacology is the science that investigates the interactions between organisms and drugs and their mechanisms. Pharmacology plays a translational role in modern medicine, bridging basic research and the clinic. With its economy booming, China has invested an enormous amount of financial and human resources in pharmacological research in the recent decade. As a result, major breakthroughs have been achieved in both basic and clinical research, with the discovery of many potential drug targets and biomarkers that has made a sizable contribution to the overall advancement of pharmacological sciences. In this article, we review recent research efforts and representative scientific achievements and discuss future challenges and directions for the pharmacological sciences in China.
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Affiliation(s)
- Jian-Cheng Wang
- Department of Health Sciences, National Natural Science Foundation of China (J.-C.W., Y.Z., L.W., E.D.) and School of Pharmaceutical Sciences, Peking University (J.-C.W.), Beijing, China
| | - Yuangui Zhu
- Department of Health Sciences, National Natural Science Foundation of China (J.-C.W., Y.Z., L.W., E.D.) and School of Pharmaceutical Sciences, Peking University (J.-C.W.), Beijing, China
| | - Lei Wu
- Department of Health Sciences, National Natural Science Foundation of China (J.-C.W., Y.Z., L.W., E.D.) and School of Pharmaceutical Sciences, Peking University (J.-C.W.), Beijing, China
| | - Erdan Dong
- Department of Health Sciences, National Natural Science Foundation of China (J.-C.W., Y.Z., L.W., E.D.) and School of Pharmaceutical Sciences, Peking University (J.-C.W.), Beijing, China
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218
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El-Habr EA, Dubois LG, Burel-Vandenbos F, Bogeas A, Lipecka J, Turchi L, Lejeune FX, Coehlo PLC, Yamaki T, Wittmann BM, Fareh M, Mahfoudhi E, Janin M, Narayanan A, Morvan-Dubois G, Schmitt C, Verreault M, Oliver L, Sharif A, Pallud J, Devaux B, Puget S, Korkolopoulou P, Varlet P, Ottolenghi C, Plo I, Moura-Neto V, Virolle T, Chneiweiss H, Junier MP. A driver role for GABA metabolism in controlling stem and proliferative cell state through GHB production in glioma. Acta Neuropathol 2017; 133:645-660. [PMID: 28032215 PMCID: PMC5348560 DOI: 10.1007/s00401-016-1659-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 12/15/2016] [Accepted: 12/15/2016] [Indexed: 12/30/2022]
Abstract
Cell populations with differing proliferative, stem-like and tumorigenic states co-exist in most tumors and especially malignant gliomas. Whether metabolic variations can drive this heterogeneity by controlling dynamic changes in cell states is unknown. Metabolite profiling of human adult glioblastoma stem-like cells upon loss of their tumorigenicity revealed a switch in the catabolism of the GABA neurotransmitter toward enhanced production and secretion of its by-product GHB (4-hydroxybutyrate). This switch was driven by succinic semialdehyde dehydrogenase (SSADH) downregulation. Enhancing GHB levels via SSADH downregulation or GHB supplementation triggered cell conversion into a less aggressive phenotypic state. GHB affected adult glioblastoma cells with varying molecular profiles, along with cells from pediatric pontine gliomas. In all cell types, GHB acted by inhibiting α-ketoglutarate-dependent Ten–eleven Translocations (TET) activity, resulting in decreased levels of the 5-hydroxymethylcytosine epigenetic mark. In patients, low SSADH expression was correlated with high GHB/α-ketoglutarate ratios, and distinguished weakly proliferative/differentiated glioblastoma territories from proliferative/non-differentiated territories. Our findings support an active participation of metabolic variations in the genesis of tumor heterogeneity.
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219
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Nickerson ML, Das S, Im KM, Turan S, Berndt SI, Li H, Lou H, Brodie SA, Billaud JN, Zhang T, Bouk AJ, Butcher D, Wang Z, Sun L, Misner K, Tan W, Esnakula A, Esposito D, Huang WY, Hoover RN, Tucker MA, Keller JR, Boland J, Brown K, Anderson SK, Moore LE, Isaacs WB, Chanock SJ, Yeager M, Dean M, Andresson T. TET2 binds the androgen receptor and loss is associated with prostate cancer. Oncogene 2017; 36:2172-2183. [PMID: 27819678 PMCID: PMC5391277 DOI: 10.1038/onc.2016.376] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 08/15/2016] [Accepted: 08/29/2016] [Indexed: 12/11/2022]
Abstract
Genetic alterations associated with prostate cancer (PCa) may be identified by sequencing metastatic tumour genomes to identify molecular markers at this lethal stage of disease. Previously, we characterized somatic alterations in metastatic tumours in the methylcytosine dioxygenase ten-eleven translocation 2 (TET2), which is altered in 5-15% of myeloid, kidney, colon and PCas. Genome-wide association studies previously identified non-coding risk variants associated with PCa and melanoma. We perform fine-mapping of PCa risk across TET2 using genotypes from the PEGASUS case-control cohort and identify six new risk variants in introns 1 and 2. Oligonucleotides containing two risk variants are bound by the transcription factor octamer-binding protein 1 (Oct1/POU2F1) and TET2 and Oct1 expression are positively correlated in prostate tumours. TET2 is expressed in normal prostate tissue and reduced in a subset of tumours from the Cancer Genome Atlas (TCGA). Small interfering RNA-mediated TET2 knockdown (KD) increases LNCaP cell proliferation, migration and wound healing, verifying loss drives a cancer phenotype. Endogenous TET2 bound the androgen receptor (AR) and AR-coactivator proteins in LNCaP cell extracts, and TET2 KD increases prostate-specific antigen (KLK3/PSA) expression. Published data reveal TET2 binding sites and hydroxymethylcytosine proximal to KLK3. A gene co-expression network identified using TCGA prostate tumour RNA-sequencing identifies co-regulated cancer genes associated with 2-oxoglutarate (2-OG) and succinate metabolism, including TET2, lysine demethylase (KDM) KDM6A, BRCA1-associated BAP1, and citric acid cycle enzymes IDH1/2, SDHA/B, and FH. The co-expression signature is conserved across 31 TCGA cancers suggesting a putative role for TET2 as an energy sensor (of 2-OG) that modifies aspects of androgen-AR signalling. Decreased TET2 mRNA expression in TCGA PCa tumours is strongly associated with reduced patient survival, indicating reduced expression in tumours may be an informative biomarker of disease progression and perhaps metastatic disease.
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Affiliation(s)
- M L Nickerson
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - S Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - K M Im
- Data Science for Genomics, Ellicott City, MD, USA
| | - S Turan
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - S I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - H Li
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Basic Research Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - H Lou
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Basic Research Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - S A Brodie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - J N Billaud
- Ingenuity Systems, Inc., Redwood City, CA, USA
| | - T Zhang
- Laboratory of Translational Genomics, National Cancer Institute, Bethesda, MD, USA
| | - A J Bouk
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - D Butcher
- Pathology and Histotechnology Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Z Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - L Sun
- Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - K Misner
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - W Tan
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Basic Research Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - A Esnakula
- Department of Pathology, Howard University College of Medicine, Howard University Hospital, NW, Washington, DC, USA
| | - D Esposito
- Protein Expression Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - W Y Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - R N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - M A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - J R Keller
- Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - J Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - K Brown
- Laboratory of Translational Genomics, National Cancer Institute, Bethesda, MD, USA
| | - S K Anderson
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - L E Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - W B Isaacs
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - S J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - M Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - M Dean
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - T Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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220
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Lee M, Li J, Liang Y, Ma G, Zhang J, He L, Liu Y, Li Q, Li M, Sun D, Zhou Y, Huang Y. Engineered Split-TET2 Enzyme for Inducible Epigenetic Remodeling. J Am Chem Soc 2017; 139:4659-4662. [PMID: 28294608 PMCID: PMC5385525 DOI: 10.1021/jacs.7b01459] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Ten-eleven translocation (TET) family of 5-methylcytosine (5mC) dioxygenases catalyze the conversion of 5mC into 5-hydroxymethylcytosine (5hmC) and further oxidized species to promote active DNA demethylation. Here we engineered a split-TET2 enzyme to enable temporal control of 5mC oxidation and subsequent remodeling of epigenetic states in mammalian cells. We further demonstrate the use of this chemically inducible system to dissect the correlation between DNA hydroxymethylation and chromatin accessibility in the mammalian genome. This chemical-inducible epigenome remodeling tool will find broad use in interrogating cellular systems without altering the genetic code, as well as in probing the epigenotype-phenotype relations in various biological systems.
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Affiliation(s)
- Minjung Lee
- Centre for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University , 2121 W Holcombe Boulevard, Houston, Texas 77030, United States
| | - Jia Li
- Centre for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University , 2121 W Holcombe Boulevard, Houston, Texas 77030, United States
| | - Yi Liang
- Centre for Translational Cancer Research, Institute of Biosciences and Technology, Department of Medical Physiology, College of Medicine, Texas A&M University , 2121 W Holcombe Boulevard, Houston, Texas 77030, United States
| | - Guolin Ma
- Centre for Translational Cancer Research, Institute of Biosciences and Technology, Department of Medical Physiology, College of Medicine, Texas A&M University , 2121 W Holcombe Boulevard, Houston, Texas 77030, United States
| | - Jixiang Zhang
- Centre for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University , 2121 W Holcombe Boulevard, Houston, Texas 77030, United States.,Department of Gastroenterology, Renmin Hospital of Wuhan University , Wuhan, Hubei 430060, China
| | - Lian He
- Centre for Translational Cancer Research, Institute of Biosciences and Technology, Department of Medical Physiology, College of Medicine, Texas A&M University , 2121 W Holcombe Boulevard, Houston, Texas 77030, United States
| | - Yuliang Liu
- Centre for Translational Cancer Research, Institute of Biosciences and Technology, Department of Medical Physiology, College of Medicine, Texas A&M University , 2121 W Holcombe Boulevard, Houston, Texas 77030, United States
| | - Qian Li
- Centre for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University , 2121 W Holcombe Boulevard, Houston, Texas 77030, United States
| | - Minyong Li
- School of Pharmacy, Shandong University , 44 Wenhua Road W., Jinan, Shandong 250012, China
| | - Deqiang Sun
- Centre for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University , 2121 W Holcombe Boulevard, Houston, Texas 77030, United States
| | - Yubin Zhou
- Centre for Translational Cancer Research, Institute of Biosciences and Technology, Department of Medical Physiology, College of Medicine, Texas A&M University , 2121 W Holcombe Boulevard, Houston, Texas 77030, United States
| | - Yun Huang
- Centre for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University , 2121 W Holcombe Boulevard, Houston, Texas 77030, United States
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221
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Jaiswal M, Bhar S, Vemula H, Prakash S, Ponnaluri VKC, Gutheil WG, Mukherji M. Convenient expression, purification and quantitative liquid chromatography-tandem mass spectrometry-based analysis of TET2 5-methylcytosine demethylase. Protein Expr Purif 2017; 132:143-151. [PMID: 28188826 DOI: 10.1016/j.pep.2017.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/26/2016] [Accepted: 02/03/2017] [Indexed: 10/20/2022]
Abstract
5-Methylcytosine within CpG islands in DNA plays a crucial role in epigenetic transcriptional regulation during metazoan development. Recently, it has been established that the Ten-Eleven Translocation (TET) family, Fe(II)- and 2-oxoglutarate (2OG/αKG)-dependent oxygenases initiate 5-methylcytosine demethylation by iterative oxidation reactions. Mutations in the TET2 gene are frequently detected in patients with myeloid malignancies. Here, we describe the cloning of untagged human TET2 demethylase using Gateway technology and its efficient expression in E. coli. The untagged TET2 enzyme was purified using cation exchange and heparin sepharose chromatography. In addition, a reliable quantitative liquid chromatography-tandem mass spectrometry-based assay was utilized to analyze the activity of TET2 oxygenase. This assay was further used to analyze the activity of a number of clinical TET2 variants with mutations in the 2OG binding sites. Our results demonstrate that the activity of one TET2 mutant, TET2-R1896S, can be restored using an excess of 2OG in the reaction mixture. These studies suggest that dietary 2OG supplements, which are commonly used for several other conditions, may be used to treat some patients with myeloid malignancies harboring TET2-R1896S mutation. Results described in this paper serve as a foundation for better characterization of wild type as well as mutant TET2 demethylases.
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Affiliation(s)
- Mohit Jaiswal
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Subhradeep Bhar
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Harika Vemula
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Swami Prakash
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - V K Chaithanya Ponnaluri
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - William G Gutheil
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Mridul Mukherji
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA.
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222
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Cimmino L, Aifantis I. Alternative roles for oxidized mCs and TETs. Curr Opin Genet Dev 2016; 42:1-7. [PMID: 27939598 DOI: 10.1016/j.gde.2016.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/15/2016] [Indexed: 01/09/2023]
Abstract
Ten-eleven-translocation (TET) proteins oxidize 5-methylcytosine (5mC) to form stable or transient modifications (oxi-mCs) in the mammalian genome. Genome-wide mapping and protein interaction studies have shown that 5mC and oxi-mCs have unique distribution patterns and alternative roles in gene expression. In addition, oxi-mCs may interact with specific chromatin regulators, transcription factors and DNA repair proteins to maintain genomic integrity or alter DNA replication and transcriptional elongation rates. In this review we will discuss recent advances in our understanding of how TETs and 5hmC exert their epigenetic function as tumor suppressors by playing alternative roles in transcriptional regulation and genomic stability.
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Affiliation(s)
- Luisa Cimmino
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA.
| | - Iannis Aifantis
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA
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223
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Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine. Nat Chem Biol 2016; 13:181-187. [PMID: 27918559 DOI: 10.1038/nchembio.2250] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 09/29/2016] [Indexed: 12/16/2022]
Abstract
Ten-eleven translocation (TET) enzymes catalyze stepwise oxidation of 5-methylcytosine (mC) to yield 5-hydroxymethylcytosine (hmC) and the rarer bases 5-formylcytosine (fC) and 5-carboxylcytosine (caC). Stepwise oxidation obscures how each individual base forms and functions in epigenetic regulation, and prompts the question of whether TET enzymes primarily serve to generate hmC or are adapted to produce fC and caC as well. By mutating a single, conserved active site residue in human TET2, Thr1372, we uncovered enzyme variants that permit oxidation to hmC but largely eliminate fC and caC. Biochemical analyses, combined with molecular dynamics simulations, elucidated an active site scaffold that is required for wild-type (WT) stepwise oxidation and that, when perturbed, explains the mutants' hmC-stalling phenotype. Our results suggest that the TET2 active site is shaped to enable higher-order oxidation and provide the first TET variants that could be used to probe the biological functions of hmC separately from fC and caC.
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224
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Affiliation(s)
- Hao Cheng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
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225
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Chiba S. Dysregulation of TET2 in hematologic malignancies. Int J Hematol 2016; 105:17-22. [PMID: 27848178 DOI: 10.1007/s12185-016-2122-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 10/31/2016] [Indexed: 12/11/2022]
Abstract
The TET dioxygenases, TET1, TET2, and TET3, catalyze transfer of an oxygen atom to the methyl group of 5-methylcytocine (5-mC), converting it to 5-hydroxymethylcytocine (5-hmC). Among the genes encoding these enzymes, ten-eleven translocation 2 (TET2) is frequently mutated somatically in both myeloid and lymphoid malignancies. Because these TET2 mutations result in the impairment of the dioxygenase activity of TET2, it is thought that these mutations interfere with 5-mC to 5-hmC conversion. There is ample evidence indicating that TET2 mutations are a driver of tumorigenesis in blood cells and that TET2 mutations are often acquired at the hematopoietic stem/early progenitor cell stage. In addition, TET2 is the second-most frequently mutated gene in clonal hematopoiesis in individuals with no apparent blood cancers, suggesting that while TET2 mutations alone are insufficient to cause hematologic malignancy, they represent an early event during tumorigenesis. A number of questions, including the precise target genome regions of TET2, and the importance of the balance of 5-mC and 5-hmC in the regulatory regions in transcriptional control, remain.
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Affiliation(s)
- Shigeru Chiba
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.
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226
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Koboldt DC, Kanchi KL, Gui B, Larson DE, Fulton RS, Isaacs WB, Kraja A, Borecki IB, Jia L, Wilson RK, Mardis ER, Kibel AS. Rare Variation in TET2 Is Associated with Clinically Relevant Prostate Carcinoma in African Americans. Cancer Epidemiol Biomarkers Prev 2016; 25:1456-1463. [PMID: 27486019 PMCID: PMC5093030 DOI: 10.1158/1055-9965.epi-16-0373] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/20/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Common variants have been associated with prostate cancer risk. Unfortunately, few are reproducibly linked to aggressive disease, the phenotype of greatest clinical relevance. One possible explanation is that rare genetic variants underlie a significant proportion of the risk for aggressive disease. METHOD To identify such variants, we performed a two-stage approach using whole-exome sequencing followed by targeted sequencing of 800 genes in 652 aggressive prostate cancer patients and 752 disease-free controls in both African and European Americans. In each population, we tested rare variants for association using two gene-based aggregation tests. We established a study-wide significance threshold of 3.125 × 10-5 to correct for multiple testing. RESULTS TET2 in African Americans was associated with aggressive disease, with 24.4% of cases harboring a rare deleterious variant compared with 9.6% of controls (FET P = 1.84 × 10-5, OR = 3.0; SKAT-O P = 2.74 × 10-5). We report 8 additional genes with suggestive evidence of association, including the DNA repair genes PARP2 and MSH6 Finally, we observed an excess of rare truncation variants in 5 genes, including the DNA repair genes MSH6, BRCA1, and BRCA2 This adds to the growing body of evidence that DNA repair pathway defects may influence susceptibility to aggressive prostate cancer. CONCLUSIONS Our findings suggest that rare variants influence risk of clinically relevant prostate cancer and, if validated, could serve to identify men for screening, prophylaxis, and treatment. IMPACT This study provides evidence that rare variants in TET2 may help identify African American men at increased risk for clinically relevant prostate cancer. Cancer Epidemiol Biomarkers Prev; 25(11); 1456-63. ©2016 AACR.
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Affiliation(s)
- Daniel C Koboldt
- The McDonnell Genome Institute at Washington University, St. Louis, Missouri
| | - Krishna L Kanchi
- The McDonnell Genome Institute at Washington University, St. Louis, Missouri
| | - Bin Gui
- Division of Urology, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - David E Larson
- The McDonnell Genome Institute at Washington University, St. Louis, Missouri
| | - Robert S Fulton
- The McDonnell Genome Institute at Washington University, St. Louis, Missouri
| | - William B Isaacs
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University, Baltimore, Maryland
| | - Aldi Kraja
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri
| | - Ingrid B Borecki
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri
| | - Li Jia
- Division of Urology, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Richard K Wilson
- The McDonnell Genome Institute at Washington University, St. Louis, Missouri
| | - Elaine R Mardis
- The McDonnell Genome Institute at Washington University, St. Louis, Missouri
| | - Adam S Kibel
- Division of Urology, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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227
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Lu J, Hu L, Cheng J, Fang D, Wang C, Yu K, Jiang H, Cui Q, Xu Y, Luo C. A computational investigation on the substrate preference of ten-eleven-translocation 2 (TET2). Phys Chem Chem Phys 2016; 18:4728-38. [PMID: 26799843 DOI: 10.1039/c5cp07266b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
TET proteins iteratively convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) in a Fe(ii)/α-ketoglutarate-dependent manner. Our previous biochemical studies revealed that TET proteins are more active on 5mC than on 5hmC and 5fC. However, the source of the substrate preference of TET proteins still remains largely elusive. Here, we investigated the substrate binding and catalytic mechanisms of oxidation reactions mediated by TET2 on different substrates through computational approaches. In accordance with previous experimental reports, our computational results suggest that TET2 can bind to different substrates with comparable binding affinities and the hydrogen abstraction step in the catalytic cycle acts as the rate-limiting step. Further structural characterization of the intermediate structures revealed that the 5-substitution groups on 5hmC and 5fC adopt an unfavorable orientation for hydrogen abstraction, which leads to a higher energy barrier for 5hmC and 5fC (compared to 5mC) and thus a lower catalytic efficiency. In summary, our mechanical insights demonstrate that substrate preference is the intrinsic property of TET proteins and our theoretical calculation results can guide further dry-lab or wet-lab studies on the catalytic mechanism of TET proteins as well as other Fe(ii)/α-ketoglutarate (KG)-dependent dioxygenases.
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Affiliation(s)
- Junyan Lu
- Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Lulu Hu
- Fudan University Shanghai Cancer Centre, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China. and State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jingdong Cheng
- Fudan University Shanghai Cancer Centre, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.
| | - Dong Fang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Ave, Madison, WI 53706, USA
| | - Chen Wang
- Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Kunqian Yu
- Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Hualiang Jiang
- Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Ave, Madison, WI 53706, USA
| | - Yanhui Xu
- Fudan University Shanghai Cancer Centre, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China. and State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Cheng Luo
- Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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228
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Zhou C, Liu Y, Li X, Zou J, Zou S. DNA N 6-methyladenine demethylase ALKBH1 enhances osteogenic differentiation of human MSCs. Bone Res 2016; 4:16033. [PMID: 27785372 PMCID: PMC5057179 DOI: 10.1038/boneres.2016.33] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 08/13/2016] [Accepted: 08/14/2016] [Indexed: 02/05/2023] Open
Abstract
ALKBH1 was recently discovered as a demethylase for DNA N6-methyladenine (N6-mA), a new epigenetic modification, and interacts with the core transcriptional pluripotency network of embryonic stem cells. However, the role of ALKBH1 and DNA N6-mA in regulating osteogenic differentiation is largely unknown. In this study, we demonstrated that the expression of ALKBH1 in human mesenchymal stem cells (MSCs) was upregulated during osteogenic induction. Knockdown of ALKBH1 increased the genomic DNA N6-mA levels and significantly reduced the expression of osteogenic-related genes, alkaline phosphatase activity, and mineralization. ALKBH1-depleted MSCs also exhibited a restricted capacity for bone formation in vivo. By contrast, the ectopic overexpression of ALKBH1 enhanced osteoblastic differentiation. Mechanically, we found that the depletion of ALKBH1 resulted in the accumulation of N6-mA on the promoter region of ATF4, which subsequently silenced ATF4 transcription. In addition, restoring the expression of ATP by adenovirus-mediated transduction successfully rescued osteogenic differentiation. Taken together, our results demonstrate that ALKBH1 is indispensable for the osteogenic differentiation of MSCs and indicate that DNA N6-mA modifications area new mechanism for the epigenetic regulation of stem cell differentiation.
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Affiliation(s)
- Chenchen Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu, China
| | - Yuting Liu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu, China
| | - Xiaobing Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu, China
| | - Jing Zou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu, China
| | - Shujuan Zou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu, China
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229
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Retinol and ascorbate drive erasure of epigenetic memory and enhance reprogramming to naïve pluripotency by complementary mechanisms. Proc Natl Acad Sci U S A 2016; 113:12202-12207. [PMID: 27729528 DOI: 10.1073/pnas.1608679113] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Epigenetic memory, in particular DNA methylation, is established during development in differentiating cells and must be erased to create naïve (induced) pluripotent stem cells. The ten-eleven translocation (TET) enzymes can catalyze the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidized derivatives, thereby actively removing this memory. Nevertheless, the mechanism by which the TET enzymes are regulated, and the extent to which they can be manipulated, are poorly understood. Here we report that retinoic acid (RA) or retinol (vitamin A) and ascorbate (vitamin C) act as modulators of TET levels and activity. RA or retinol enhances 5hmC production in naïve embryonic stem cells by activation of TET2 and TET3 transcription, whereas ascorbate potentiates TET activity and 5hmC production through enhanced Fe2+ recycling, and not as a cofactor as reported previously. We find that both ascorbate and RA or retinol promote the derivation of induced pluripotent stem cells synergistically and enhance the erasure of epigenetic memory. This mechanistic insight has significance for the development of cell treatments for regenenerative medicine, and enhances our understanding of how intrinsic and extrinsic signals shape the epigenome.
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230
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Liu YQ, Wang XL, Cheng X, Lu YZ, Wang GZ, Li XC, Zhang J, Wen ZS, Huang ZL, Gao QL, Yang LN, Cheng YX, Tao SC, Liu J, Zhou GB. Skp1 in lung cancer: clinical significance and therapeutic efficacy of its small molecule inhibitors. Oncotarget 2016; 6:34953-67. [PMID: 26474281 PMCID: PMC4741501 DOI: 10.18632/oncotarget.5547] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/29/2015] [Indexed: 12/24/2022] Open
Abstract
Skp1 is an essential adaptor protein of the Skp1-Cul1-F-box protein complex and is able to stabilize the conformation of some ubiquitin E3 ligases. However, the role Skp1 plays during tumorigenesis remains unclear and Skp1-targeting agent is lacking. Here we showed that Skp1 was overexpressed in 36/64 (56.3%) of non-small cell lung cancers, and elevated Skp1 was associated with poor prognosis. By structure-based high-throughput virtual screening, we found some Skp1-targeting molecules including a natural compound 6-O-angeloylplenolin (6-OAP). 6-OAP bound Skp1 at sites critical to Skp1-Skp2 interaction, leading to dissociation and proteolysis of oncogenic E3 ligases NIPA, Skp2, and β-TRCP, and accumulation of their substrates Cyclin B1, P27 and E-Cadherin. 6-OAP induced prometaphase arrest and exerted potent anti-lung cancer activity in two murine models and showed low adverse effect. These results indicate that Skp1 is critical to lung cancer pathogenesis, and Skp1 inhibitor inactivates crucial oncogenic E3 ligases and exhibits significant therapeutic potentials.
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Affiliation(s)
- Yong-Qiang Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao-Lu Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Cheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yong-Zhi Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Gui-Zhen Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xin-Chun Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Zhang
- School of Life Sciences, Anhui University, Hefei 230039, China
| | - Zhe-Sheng Wen
- Department of Thoracic Surgery, The Cancer Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhi-Liang Huang
- Department of Thoracic Surgery, The Cancer Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Qin-Lei Gao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Li-Na Yang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong-Xian Cheng
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Guang-Biao Zhou
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing 100101, China
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Abstract
Ten eleven translocation (TET) genes, and especially TET2, are frequently mutated in various cancers, but how the TET proteins contribute to the onset and maintenance of these malignancies is largely unknown. In this review, Rasmussen and Helin highlight recent advances in understanding the physiological function of the TET proteins and their role in regulating DNA methylation and transcription. 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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Affiliation(s)
- Kasper Dindler Rasmussen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark; The Danish Stem Cell Center (Danstem), University of Copenhagen, 2200 Copenhagen, Denmark; Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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232
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Drohat AC, Coey CT. Role of Base Excision "Repair" Enzymes in Erasing Epigenetic Marks from DNA. Chem Rev 2016; 116:12711-12729. [PMID: 27501078 DOI: 10.1021/acs.chemrev.6b00191] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Base excision repair (BER) is one of several DNA repair pathways found in all three domains of life. BER counters the mutagenic and cytotoxic effects of damage that occurs continuously to the nitrogenous bases in DNA, and its critical role in maintaining genomic integrity is well established. However, BER also performs essential functions in processes other than DNA repair, where it acts on naturally modified bases in DNA. A prominent example is the central role of BER in mediating active DNA demethylation, a multistep process that erases the epigenetic mark 5-methylcytosine (5mC), and derivatives thereof, converting them back to cytosine. Herein, we review recent advances in the understanding of how BER mediates this critical component of epigenetic regulation in plants and animals.
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Affiliation(s)
- Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Christopher T Coey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
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233
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Tamanaha E, Guan S, Marks K, Saleh L. Distributive Processing by the Iron(II)/α-Ketoglutarate-Dependent Catalytic Domains of the TET Enzymes Is Consistent with Epigenetic Roles for Oxidized 5-Methylcytosine Bases. J Am Chem Soc 2016; 138:9345-8. [PMID: 27362828 DOI: 10.1021/jacs.6b03243] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The ten-eleven translocation (TET) proteins catalyze oxidation of 5-methylcytosine ((5m)C) residues in nucleic acids to 5-hydroxymethylcytosine ((5hm)C), 5-formylcytosine ((5f)C), and 5-carboxycytosine ((5ca)C). These nucleotide bases have been implicated as intermediates on the path to active demethylation, but recent reports have suggested that they might have specific regulatory roles in their own right. In this study, we present kinetic evidence showing that the catalytic domains (CDs) of TET2 and TET1 from mouse and their homologue from Naegleria gruberi, the full-length protein NgTET1, are distributive in both chemical and physical senses, as they carry out successive oxidations of a single (5m)C and multiple (5m)C residues along a polymethylated DNA substrate. We present data showing that the enzyme neither retains (5hm)C/(5f)C intermediates of preceding oxidations nor slides along a DNA substrate (without releasing it) to process an adjacent (5m)C residue. These findings contradict a recent report by Crawford et al. ( J. Am. Chem. Soc. 2016 , 138 , 730 ) claiming that oxidation of (5m)C by CD of mouse TET2 is chemically processive (iterative). We further elaborate that this distributive mechanism is maintained for TETs in two evolutionarily distant homologues and posit that this mode of function allows the introduction of (5m)C forms as epigenetic markers along the DNA.
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Affiliation(s)
- Esta Tamanaha
- New England Biolabs, Inc. , 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Shengxi Guan
- New England Biolabs, Inc. , 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Katherine Marks
- New England Biolabs, Inc. , 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Lana Saleh
- New England Biolabs, Inc. , 240 County Road, Ipswich, Massachusetts 01938, United States
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234
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Hadad N, Masser DR, Logan S, Wronowski B, Mangold CA, Clark N, Otalora L, Unnikrishnan A, Ford MM, Giles CB, Wren JD, Richardson A, Sonntag WE, Stanford DR, Freeman W. Absence of genomic hypomethylation or regulation of cytosine-modifying enzymes with aging in male and female mice. Epigenetics Chromatin 2016; 9:30. [PMID: 27413395 PMCID: PMC4942942 DOI: 10.1186/s13072-016-0080-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/06/2016] [Indexed: 02/06/2023] Open
Abstract
Background Changes to the epigenome with aging, and DNA modifications in particular, have been proposed as a central regulator of the aging process, a predictor of mortality, and a contributor to the pathogenesis of age-related diseases. In the central nervous system, control of learning and memory, neurogenesis, and plasticity require changes in cytosine methylation and hydroxymethylation. Although genome-wide decreases in methylation with aging are often reported as scientific dogma, primary research reports describe decreases, increases, or lack of change in methylation and hydroxymethylation and their principle regulators, DNA methyltransferases and ten-eleven translocation dioxygenases in the hippocampus. Furthermore, existing data are limited to only male animals. Results Through examination of the hippocampus in young, adult, and old male and female mice by antibody-based, pyrosequencing, and whole-genome oxidative bisulfite sequencing methods, we provide compelling evidence that contradicts the genomic hypomethylation theory of aging. We also demonstrate that expression of DNA methyltransferases and ten-eleven translocation dioxygenases is not differentially regulated with aging or between the sexes, including the proposed cognitive aging regulator DNMT3a2. Using oxidative bisulfite sequencing that discriminates methylation from hydroxymethylation and by cytosine (CG and non-CG) context, we observe sex differences in average CG methylation and hydroxymethylation of the X chromosome, and small age-related differences in hydroxymethylation of CG island shores and shelves, and methylation of promoter regions. Conclusion These findings clarify a long-standing misconception of the epigenomic response to aging and demonstrate the need for studies of base-specific methylation and hydroxymethylation with aging in both sexes. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0080-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Niran Hadad
- Oklahoma Center for Neuroscience, Oklahoma City, OK USA ; Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA
| | - Dustin R Masser
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Sreemathi Logan
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA
| | - Benjamin Wronowski
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Colleen A Mangold
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA USA
| | - Nicholas Clark
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Laura Otalora
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Archana Unnikrishnan
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA
| | - Matthew M Ford
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR USA
| | - Cory B Giles
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Jonathan D Wren
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Arlan Richardson
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA ; Oklahoma City VA Medical Center, Oklahoma City, OK USA ; Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - William E Sonntag
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - David R Stanford
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Willard Freeman
- Oklahoma Center for Neuroscience, Oklahoma City, OK USA ; Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA ; Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
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235
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Tan Q, Wang W, Yang C, Zhang J, Sun K, Luo HC, Mai LF, Lao Y, Yan L, Ren M. α-ketoglutarate is associated with delayed wound healing in diabetes. Clin Endocrinol (Oxf) 2016; 85:54-61. [PMID: 26921880 DOI: 10.1111/cen.13047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 01/06/2016] [Accepted: 02/21/2016] [Indexed: 01/13/2023]
Abstract
AIM A high level of matrix metalloproteinase 9 (MMP-9) is a predictor of poor wound healing in diabetic foot ulcers. In skin keratinocytes, site-specific DNA demethylation plays an important role in MMP-9 expression. Ten-eleven translocation enzyme 2 (TET2) protein, one member of TET family, could rely on α-ketoglutarate (α-KG) as cosubstrate to exhibit catalytic activity of DNA demethylation. Here, we aimed to explore the changes of α-KG and its relationship with MMP-9 and TET2 during diabetic wound healing. METHODS Seventy-one cases of patients with diabetic foot ulcers and 53 cases of nondiabetic ulcers were enrolled. Serum, urine and wound fluids were collected for measurement of α-KG levels and MMP-9 expression. Skin tissues were collected for the measurement of TET2 and MMP-9 expression. Clinical parameters were collected, and transcutaneous oxygen pressure (TcPO2) levels of feet were detected. RESULTS The levels of α-KG, TET2 and MMP-9 were significantly increased in diabetic wound compared with nondiabetic wound (P = 0·010, 0·016 and 0·025). There was a significant correlation between a low TcPO2 and a high α-KG level of wound fluids (r = -0·395, P = 0·002). Further analysis showed that α-KG concentration had a positive correlation with both haemoglobin A1c (HbA1C) and 2 h postprandial blood glucose (PBG) (r = 0·393, P = 0·005; r = 0·320, P = 0·025, respectively). CONCLUSIONS The levels of α-KG, TET2 and MMP-9 were significantly increased in diabetic wound compared with nondiabetic wound. Elevated α-KG was related to local hypoxia ischaemia status and systematic poor glycaemic control.
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Affiliation(s)
- Qin Tan
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Wei Wang
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Chuan Yang
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Jinglu Zhang
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Kan Sun
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Heng Cong Luo
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Li Fang Mai
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Yu Lao
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Li Yan
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Meng Ren
- Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
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236
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Ludwig AK, Zhang P, Cardoso MC. Modifiers and Readers of DNA Modifications and Their Impact on Genome Structure, Expression, and Stability in Disease. Front Genet 2016; 7:115. [PMID: 27446199 PMCID: PMC4914596 DOI: 10.3389/fgene.2016.00115] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/06/2016] [Indexed: 12/16/2022] Open
Abstract
Cytosine base modifications in mammals underwent a recent expansion with the addition of several naturally occurring further modifications of methylcytosine in the last years. This expansion was accompanied by the identification of the respective enzymes and proteins reading and translating the different modifications into chromatin higher order organization as well as genome activity and stability, leading to the hypothesis of a cytosine code. Here, we summarize the current state-of-the-art on DNA modifications, the enzyme families setting the cytosine modifications and the protein families reading and translating the different modifications with emphasis on the mouse protein homologs. Throughout this review, we focus on functional and mechanistic studies performed on mammalian cells, corresponding mouse models and associated human diseases.
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Affiliation(s)
- Anne K Ludwig
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt Germany
| | - Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt Germany
| | - M C Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt Germany
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237
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Abstract
A complete understanding of the function of the ten-eleven translocation (TET) family of dioxygenase-mediated DNA demethylation requires new methods to quantitatively map oxidized 5-methylcytosine (5mC) bases at high resolution. We have recently developed a methylase-assisted bisulfite sequencing (MAB-seq) method that allows base-resolution mapping of 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), two oxidized 5mC bases indicative of active DNA demethylation events. In standard bisulfite sequencing (BS-seq), unmodified C, 5fC and 5caC are read as thymine; thus 5fC and 5caC cannot be distinguished from C. In MAB-seq, unmodified C is enzymatically converted to 5mC, allowing direct mapping of rare modifications such as 5fC and 5caC. By combining MAB-seq with chemical reduction of 5fC to 5hmC, we also developed caMAB-seq, a method for direct 5caC mapping. Compared with subtraction-based mapping methods, MAB-seq and caMAB-seq require less sequencing effort and enable robust statistical calling of 5fC and/or 5caC. MAB-seq and caMAB-seq can be adapted to map 5fC/5caC at the whole-genome scale (WG-MAB-seq), within specific genomic regions enriched for enhancer-marking histone modifications (chromatin immunoprecipitation (ChIP)-MAB-seq), or at CpG-rich sequences (reduced-representation (RR)-MAB-seq) such as gene promoters. The full protocol, including DNA preparation, enzymatic treatment, library preparation and sequencing, can be completed within 6-8 d.
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238
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Sérandour AA, Avner S, Mahé EA, Madigou T, Guibert S, Weber M, Salbert G. Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets. Genome Biol 2016; 17:56. [PMID: 27025842 PMCID: PMC4810514 DOI: 10.1186/s13059-016-0919-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/09/2016] [Indexed: 12/26/2022] Open
Abstract
Conventional techniques for single-base resolution mapping of epigenetic modifications of DNA such as 5-hydroxymethylcytosine (5hmC) rely on the sequencing of bisulfite-modified DNA. Here we present an alternative approach called SCL-exo which combines selective chemical labeling (SCL) of 5hmC in genomic DNA with exonuclease (exo) digestion of the bead-trapped modified DNA molecules. Associated with a straightforward bioinformatic analysis, this new procedure provides an unbiased and fast method for mapping this epigenetic mark at high resolution. Implemented on mouse genomic DNA from in vitro-differentiated neural precursor cells, SCL-exo sheds light on an intrinsic lack of conservation of hydroxymethylated CpGs across vertebrates.
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Affiliation(s)
| | - Stéphane Avner
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France.,Université de Rennes 1, Campus de Beaulieu, Rennes Cedex, 35042, France
| | - Elise A Mahé
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France.,Université de Rennes 1, Campus de Beaulieu, Rennes Cedex, 35042, France
| | - Thierry Madigou
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France.,Université de Rennes 1, Campus de Beaulieu, Rennes Cedex, 35042, France
| | - Sylvain Guibert
- CNRS, Université de Strasbourg, UMR7242, Biotechnologie et signalisation cellulaire, 300 bd Sébastien Brant, Illkirch cedex, 67412, France
| | - Michaël Weber
- CNRS, Université de Strasbourg, UMR7242, Biotechnologie et signalisation cellulaire, 300 bd Sébastien Brant, Illkirch cedex, 67412, France
| | - Gilles Salbert
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France. .,Université de Rennes 1, Campus de Beaulieu, Rennes Cedex, 35042, France.
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239
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Weber AR, Krawczyk C, Robertson AB, Kuśnierczyk A, Vågbø CB, Schuermann D, Klungland A, Schär P. Biochemical reconstitution of TET1-TDG-BER-dependent active DNA demethylation reveals a highly coordinated mechanism. Nat Commun 2016; 7:10806. [PMID: 26932196 PMCID: PMC4778062 DOI: 10.1038/ncomms10806] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 01/22/2016] [Indexed: 12/18/2022] Open
Abstract
Cytosine methylation in CpG dinucleotides is an epigenetic DNA modification dynamically established and maintained by DNA methyltransferases and demethylases. Molecular mechanisms of active DNA demethylation began to surface only recently with the discovery of the 5-methylcytosine (5mC)-directed hydroxylase and base excision activities of ten–eleven translocation (TET) proteins and thymine DNA glycosylase (TDG). This implicated a pathway operating through oxidation of 5mC by TET proteins, which generates substrates for TDG-dependent base excision repair (BER) that then replaces 5mC with C. Yet, direct evidence for a productive coupling of TET with BER has never been presented. Here we show that TET1 and TDG physically interact to oxidize and excise 5mC, and proof by biochemical reconstitution that the TET–TDG–BER system is capable of productive DNA demethylation. We show that the mechanism assures a sequential demethylation of symmetrically methylated CpGs, thereby avoiding DNA double-strand break formation but contributing to the mutability of methylated CpGs. Cytosine methylation is a dynamic DNA modification with the involvement of the base excision repair pathway suspected to be involved in demethylation. Here the authors show that TET1 and TDG interact to target modified bases and coordinate BER to avoid double strand breaks.
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Affiliation(s)
- Alain R Weber
- Department of Biomedicine, University of Basel, Mattenstrasse 28, Basel CH-4058, Switzerland
| | - Claudia Krawczyk
- Department of Biomedicine, University of Basel, Mattenstrasse 28, Basel CH-4058, Switzerland
| | - Adam B Robertson
- Department of Molecular Microbiology, Oslo University Hospital, Rikshospitalet, NO-0372 Oslo, Norway
| | - Anna Kuśnierczyk
- Proteomics and Metabolomics Core Facility, PROMEC, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway
| | - Cathrine B Vågbø
- Proteomics and Metabolomics Core Facility, PROMEC, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway
| | - David Schuermann
- Department of Biomedicine, University of Basel, Mattenstrasse 28, Basel CH-4058, Switzerland
| | - Arne Klungland
- Department of Molecular Microbiology, Oslo University Hospital, Rikshospitalet, NO-0372 Oslo, Norway
| | - Primo Schär
- Department of Biomedicine, University of Basel, Mattenstrasse 28, Basel CH-4058, Switzerland
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240
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López C, Bergmann AK, Paul U, Murga Penas EM, Nagel I, Betts MJ, Johansson P, Ritgen M, Baumann T, Aymerich M, Jayne S, Russell RB, Campo E, Dyer MJS, Dürig J, Siebert R. Genes encoding members of the JAK-STAT pathway or epigenetic regulators are recurrently mutated in T-cell prolymphocytic leukaemia. Br J Haematol 2016; 173:265-73. [DOI: 10.1111/bjh.13952] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/07/2015] [Indexed: 01/02/2023]
Affiliation(s)
- Cristina López
- Institute for Human Genetics; Christian-Albrechts-University Kiel & University Hospital Schleswig Holstein; Kiel Germany
| | - Anke K. Bergmann
- Institute for Human Genetics; Christian-Albrechts-University Kiel & University Hospital Schleswig Holstein; Kiel Germany
- Department of Paediatrics; Christian-Albrechts-University Kiel & University Hospital Schleswig Holstein; Kiel Germany
| | - Ulrike Paul
- Institute for Human Genetics; Christian-Albrechts-University Kiel & University Hospital Schleswig Holstein; Kiel Germany
| | - Eva M. Murga Penas
- Institute for Human Genetics; Christian-Albrechts-University Kiel & University Hospital Schleswig Holstein; Kiel Germany
| | - Inga Nagel
- Institute for Human Genetics; Christian-Albrechts-University Kiel & University Hospital Schleswig Holstein; Kiel Germany
| | - Matthew J. Betts
- Cell Networks; Bioquant; University of Heidelberg; Heidelberg Germany
| | - Patricia Johansson
- Department of Haematology; University Hospital Essen; University of Duisburg-Essen; Essen Germany
- Faculty of Medicine; Institute of Cell Biology (Cancer Research); University of Duisburg-Essen; Essen Germany
| | - Matthias Ritgen
- Second Department of Medicine; University Hospital of Schleswig-Holstein; Kiel Germany
| | - Tycho Baumann
- Department of Haematology; Hospital Clínic; Institut d′Investigaciones Biomèdiques August Pi I Sunyer (IDIBAPS); Barcelona Spain
| | - Marta Aymerich
- Haematopathology Unit; Hospital Clínic; Institut d′Investigaciones Biomèdiques August Pi I Sunyer (IDIBAPS); University of Barcelona; Barcelona Spain
| | - Sandrine Jayne
- Ernest and Helen Scott Haematological Research Institute; University of Leicester; Leicester UK
| | - Robert B. Russell
- Cell Networks; Bioquant; University of Heidelberg; Heidelberg Germany
| | - Elias Campo
- Haematopathology Unit; Hospital Clínic; Institut d′Investigaciones Biomèdiques August Pi I Sunyer (IDIBAPS); University of Barcelona; Barcelona Spain
| | - Martin JS Dyer
- Ernest and Helen Scott Haematological Research Institute; University of Leicester; Leicester UK
| | - Jan Dürig
- Department of Haematology; University Hospital Essen; University of Duisburg-Essen; Essen Germany
- German Cancer Consortium (DKTK); Heidelberg Germany
| | - Reiner Siebert
- Institute for Human Genetics; Christian-Albrechts-University Kiel & University Hospital Schleswig Holstein; Kiel Germany
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241
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Abstract
In eukaryotic DNA, cytosine can be enzymatically modified to yield up to four epigenetic base variants. DNA methyltransferases convert cytosine to 5-methylcytosine (mC), which plays critical roles in gene regulation during development. Ten-eleven translocation (TET) enzymes can sequentially oxidize mC to three products: 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxylcytosine (caC). These oxidized bases have been found in numerous mammalian cell types, where they potentially carry out independent epigenetic functions and aid in DNA demethylation. To gain insight into the mechanisms and functions of TET family enzymes, rigorous approaches are needed to quantify genomic cytosine modifications in cells and track TET enzyme activity in vitro. Here, we present tools developed by our lab and others to report on each of the five forms of cytosine (unmodified, mC, hmC, fC, and caC) with high specificity and sensitivity. We provide detailed protocols for qualitative and quantitative analysis of cytosine modifications in genomic DNA by dot blotting and LC-MS/MS. We then describe methods for generating synthetic oligonucleotide substrates for biochemical studies, provide optimized reaction conditions, and introduce several chemoenzymatic assays, as well as HPLC, mass spectrometry, and scintillation counting methods to quantify cytosine modifications in vitro. These approaches enable mechanistic studies of TET activity, which are key to understanding the role of these enzymes in epigenetic regulation.
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242
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Portraits of TET-mediated DNA hydroxymethylation in cancer. Curr Opin Genet Dev 2016; 36:16-26. [DOI: 10.1016/j.gde.2016.01.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/19/2016] [Accepted: 01/19/2016] [Indexed: 12/28/2022]
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243
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Peng L, Li Y, Xi Y, Li W, Li J, Lv R, Zhang L, Zou Q, Dong S, Luo H, Wu F, Yu W. MBD3L2 promotes Tet2 enzymatic activity for mediating 5-methylcytosine oxidation. J Cell Sci 2016; 129:1059-71. [PMID: 26769901 DOI: 10.1242/jcs.179044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/10/2016] [Indexed: 12/25/2022] Open
Abstract
Ten-eleven translocation (Tet) proteins are key players involved in the dynamic regulation of cytosine methylation and demethylation. Inactivating mutations of Tet2 are frequently found in human malignancies, highlighting the essential role of Tet2 in cellular transformation. However, the factors that control Tet enzymatic activity remain largely unknown. Here, we found that methyl-CpG-binding domain protein 3 (MBD3) and its homolog MBD3-like 2 (MBD3L2) can specifically modulate the enzymatic activity of Tet2 protein, but not Tet1 and Tet3 proteins, in converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). Moreover, MBD3L2 is more effective than MBD3 in promoting Tet2 enzymatic activity through strengthening the binding affinity between Tet2 and the methylated DNA target. Further analysis revealed pronounced decreases in 5mC levels at MBD3L2 and Tet2 co-occupied genomic regions, most of which are promoter elements associated with either cancer-related genes or genes involved in the regulation of cellular metabolic processes. Our data add new insights into the regulation of Tet2 activity by MBD3 and MBD3L2, and into how that affects Tet2-mediated modulation of its target genes in cancer development. Thus, they have important applications in understanding how dysregulation of Tet2 might contribute to human malignancy.
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Affiliation(s)
- Lina Peng
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Yan Li
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Yanping Xi
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Wei Li
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Jin Li
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Ruitu Lv
- Laboratory of Epigenetics, School of Basic Medicine and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Lei Zhang
- Biomedical Core Facility, School of Basic Medicine and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Qingping Zou
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Shihua Dong
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Huaibing Luo
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Feizhen Wu
- Laboratory of Epigenetics, School of Basic Medicine and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Wenqiang Yu
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200032, China
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244
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Jin SG, Zhang ZM, Dunwell TL, Harter MR, Wu X, Johnson J, Li Z, Liu J, Szabó PE, Lu Q, Xu GL, Song J, Pfeifer GP. Tet3 Reads 5-Carboxylcytosine through Its CXXC Domain and Is a Potential Guardian against Neurodegeneration. Cell Rep 2016; 14:493-505. [PMID: 26774490 DOI: 10.1016/j.celrep.2015.12.044] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/06/2015] [Accepted: 12/04/2015] [Indexed: 11/29/2022] Open
Abstract
We report that the mammalian 5-methylcytosine (5mC) oxidase Tet3 exists as three major isoforms and characterized the full-length isoform containing an N-terminal CXXC domain (Tet3FL). This CXXC domain binds to unmethylated CpGs, but, unexpectedly, its highest affinity is toward 5-carboxylcytosine (5caC). We determined the crystal structure of the CXXC domain-5caC-DNA complex, revealing the structural basis of the binding specificity of this domain as a reader of CcaCG sequences. Mapping of Tet3FL in neuronal cells shows that Tet3FL is localized precisely at the transcription start sites (TSSs) of genes involved in lysosome function, mRNA processing, and key genes of the base excision repair pathway. Therefore, Tet3FL may function as a regulator of 5caC removal by base excision repair. Active removal of accumulating 5mC from the TSSs of genes coding for lysosomal proteins by Tet3FL in postmitotic neurons of the brain may be important for preventing neurodegenerative diseases.
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Affiliation(s)
- Seung-Gi Jin
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA; Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Zhi-Min Zhang
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Thomas L Dunwell
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Matthew R Harter
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Xiwei Wu
- Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Jennifer Johnson
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Zheng Li
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiancheng Liu
- Department of Neurosciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Piroska E Szabó
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA; Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Qiang Lu
- Department of Neurosciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Guo-Liang Xu
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA.
| | - Gerd P Pfeifer
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA; Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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245
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Hong S, Cheng X. DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:321-341. [PMID: 27826845 DOI: 10.1007/978-3-319-43624-1_14] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The modification of DNA bases is a classic hallmark of epigenetics. Four forms of modified cytosine-5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine-have been discovered in eukaryotic DNA. In addition to cytosine carbon-5 modifications, cytosine and adenine methylated in the exocyclic amine-N4-methylcytosine and N6-methyladenine-are other modified DNA bases discovered even earlier. Each modified base can be considered a distinct epigenetic signal with broader biological implications beyond simple chemical changes. Since 1994, crystal structures of proteins and enzymes involved in writing, reading, and erasing modified bases have become available. Here, we present a structural synopsis of writers, readers, and erasers of the modified bases from prokaryotes and eukaryotes. Despite significant differences in structures and functions, they are remarkably similar regarding their engagement in flipping a target base/nucleotide within DNA for specific recognitions and/or reactions. We thus highlight base flipping as a common structural framework broadly applied by distinct classes of proteins and enzymes across phyla for epigenetic regulations of DNA.
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Affiliation(s)
- Samuel Hong
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA. .,Molecular and Systems Pharmacology Graduate Program, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA.
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA
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246
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Akahori H, Guindon S, Yoshizaki S, Muto Y. Molecular Evolution of the TET Gene Family in Mammals. Int J Mol Sci 2015; 16:28472-85. [PMID: 26633372 PMCID: PMC4691057 DOI: 10.3390/ijms161226110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/10/2015] [Accepted: 11/18/2015] [Indexed: 11/21/2022] Open
Abstract
Ten-eleven translocation (TET) proteins, a family of Fe2+- and 2-oxoglutarate-dependent dioxygenases, are involved in DNA demethylation. They also help regulate various cellular functions. Three TET paralogs have been identified (TET1, TET2, and TET3) in humans. This study focuses on the evolution of mammalian TET genes. Distinct patterns in TET1 and TET2 vs. TET3 were revealed by codon-based tests of positive selection. Results indicate that TET1 and TET2 genes have experienced positive selection more frequently than TET3 gene, and that the majority of codon sites evolved under strong negative selection. These findings imply that the selective pressure on TET3 may have been relaxed in several lineages during the course of evolution. Our analysis of convergent amino acid substitutions also supports the different evolutionary dynamics among TET gene subfamily members. All of the five amino acid sites that are inferred to have evolved under positive selection in the catalytic domain of TET2 are localized at the protein’s outer surface. The adaptive changes of these positively selected amino acid sites could be associated with dynamic interactions between other TET-interacting proteins, and positive selection thus appears to shift the regulatory scheme of TET enzyme function.
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Affiliation(s)
- Hiromichi Akahori
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan.
| | - Stéphane Guindon
- Department of Statistics, the University of Auckland, Auckland 1010, New Zealand.
| | - Sumio Yoshizaki
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan.
| | - Yoshinori Muto
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan.
- Department of Functional Bioscience, Gifu University School of Medicine, 1-1 Yanagido, Gifu 501-1193, Japan.
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247
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Xue JH, Xu GF, Gu TP, Chen GD, Han BB, Xu ZM, Bjørås M, Krokan HE, Xu GL, Du YR. Uracil-DNA Glycosylase UNG Promotes Tet-mediated DNA Demethylation. J Biol Chem 2015; 291:731-8. [PMID: 26620559 DOI: 10.1074/jbc.m115.693861] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Indexed: 01/10/2023] Open
Abstract
In mammals, active DNA demethylation involves oxidation of 5-methylcytosine (5mC) into 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) by Tet dioxygenases and excision of these two oxidized bases by thymine DNA glycosylase (TDG). Although TDG is essential for active demethylation in embryonic stem cells and induced pluripotent stem cells, it is hardly expressed in mouse zygotes and dispensable in pronuclear DNA demethylation. To search for other factors that might contribute to demethylation in mammalian cells, we performed a functional genomics screen based on a methylated luciferase reporter assay. UNG2, one of the glycosylases known to excise uracil residues from DNA, was found to reduce DNA methylation, thus activating transcription of a methylation-silenced reporter gene when co-transfected with Tet2 into HEK293T cells. Interestingly, UNG2 could decrease 5caC from the genomic DNA and a reporter plasmid in transfected cells, like TDG. Furthermore, deficiency in Ung partially impaired DNA demethylation in mouse zygotes. Our results suggest that UNG might be involved in Tet-mediated DNA demethylation.
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Affiliation(s)
- Jian-Huang Xue
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Gui-Fang Xu
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China, the School of Life Science, Fudan University, Shanghai 200433, China
| | - Tian-Peng Gu
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guo-Dong Chen
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bin-Bin Han
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhi-Mei Xu
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Magnar Bjørås
- the Department of Microbiology, Clinic for Diagnostics and Intervention, Oslo University Hospital, Rikshospitalet, P. O. Box 4950, Nydalen, N-0424 Oslo, Norway
| | - Hans E Krokan
- the Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway, and
| | - Guo-Liang Xu
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China, the School of Life Science and Technology, ShanghaiTech University, 319 Yue Yang Road, Shanghai 200031, China
| | - Ya-Rui Du
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China,
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248
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Wang R, Ranganathan SV, Valsangkar VA, Magliocco SM, Shen F, Chen A, Sheng J. Water-bridged hydrogen bond formation between 5-hydroxylmethylcytosine (5-hmC) and its 3'-neighbouring bases in A- and B-form DNA duplexes. Chem Commun (Camb) 2015; 51:16389-92. [PMID: 26411524 DOI: 10.1039/c5cc06563a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
5-Hydroxylmethylcytosine (5hmC) has been recognized as the sixth base with important biological functions in many tissues and cell types. We present here the high-resolution crystal structures and molecular simulation studies of both A-form and B-form DNA duplexes containing 5hmC. We observed that 5hmC interacts with its 3'-neighboring bases through water-bridged hydrogen bonds and these interactions may affect the further oxidation of 5hmC.
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Affiliation(s)
- Rui Wang
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Srivathsan V Ranganathan
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Vibhav A Valsangkar
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Stephanie M Magliocco
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Fusheng Shen
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Alan Chen
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Jia Sheng
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY 12222, USA.
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249
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Han JA, An J, Ko M. Functions of TET Proteins in Hematopoietic Transformation. Mol Cells 2015; 38:925-35. [PMID: 26552488 PMCID: PMC4673406 DOI: 10.14348/molcells.2015.0294] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/04/2015] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is a well-characterized epigenetic modification that plays central roles in mammalian development, genomic imprinting, X-chromosome inactivation and silencing of retrotransposon elements. Aberrant DNA methylation pattern is a characteristic feature of cancers and associated with abnormal expression of oncogenes, tumor suppressor genes or repair genes. Ten-eleven-translocation (TET) proteins are recently characterized dioxygenases that catalyze progressive oxidation of 5-methylcytosine to produce 5-hydroxymethylcytosine and further oxidized derivatives. These oxidized methylcytosines not only potentiate DNA demethylation but also behave as independent epigenetic modifications per se. The expression or activity of TET proteins and DNA hydroxymethylation are highly dysregulated in a wide range of cancers including hematologic and non-hematologic malignancies, and accumulating evidence points TET proteins as a novel tumor suppressor in cancers. Here we review DNA demethylation-dependent and -independent functions of TET proteins. We also describe diverse TET loss-of-function mutations that are recurrently found in myeloid and lymphoid malignancies and their potential roles in hematopoietic transformation. We discuss consequences of the deficiency of individual Tet genes and potential compensation between different Tet members in mice. Possible mechanisms underlying facilitated oncogenic transformation of TET-deficient hematopoietic cells are also described. Lastly, we address non-mutational mechanisms that lead to suppression or inactivation of TET proteins in cancers. Strategies to restore normal 5mC oxidation status in cancers by targeting TET proteins may provide new avenues to expedite the development of promising anti-cancer agents.
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Affiliation(s)
- Jae-A Han
- School of Life Sciences, Ulsan National Institute of Science and Technology
| | - Jungeun An
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 689-798,
Korea
| | - Myunggon Ko
- School of Life Sciences, Ulsan National Institute of Science and Technology
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250
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Abstract
DNA N(6)-adenine methylation (N(6)-methyladenine; 6mA) in prokaryotes functions primarily in the host defence system. The prevalence and significance of this modification in eukaryotes had been unclear until recently. Here, we discuss recent publications documenting the presence of 6mA in Chlamydomonas reinhardtii, Drosophila melanogaster and Caenorhabditis elegans; consider possible roles for this DNA modification in regulating transcription, the activity of transposable elements and transgenerational epigenetic inheritance; and propose 6mA as a new epigenetic mark in eukaryotes.
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