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      TET family dioxygenases and DNA demethylation in stem cells and cancers

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      https://www.riss.kr/link?id=A103639264

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      다국어 초록 (Multilingual 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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      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...

      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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      참고문헌 (Reference)

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      1 Borst P, "discovery, biosynthesis, and possible functions" 62 : 235-251, 2008

      2 Long HK, "ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection" 41 : 727-740, 2013

      3 Hashimoto H, "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence" 28 : 2304-2313, 2014

      4 Chen J, "Vitamin C modulates TET1 function during somatic cell reprogramming" 45 : 1504-1509, 2013

      5 Blaschke K, "Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells" 500 : 222-226, 2013

      6 Esteban MA, "Vitamin C enhances the generation of mouse and human induced pluripotent stem cells" 6 : 71-79, 2010

      7 Bostick M, "UHRF1plays a role in maintaining DNA methylation in mammalian cells" 317 : 1760-1764, 2007

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      31 Ko M, "TET proteins and 5-methylcytosine oxidation in hematological cancers" 263 : 6-21, 2015

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      42 Lu F, "Role of Tet proteins in enhancer activity and telomere elongation" 28 : 2103-2119, 2014

      43 Ito S, "Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification" 466 : 1129-1133, 2010

      44 Rasmussen KD, "Role of TET enzymes in DNA methylation, development, and cancer" 30 : 733-750, 2016

      45 Wu H, "Reversing DNA methylation: mechanisms, genomics, and biological functions" 156 : 45-68, 2014

      46 Jones PA, "Rethinking how DNA methylation patterns are maintained" 10 : 805-811, 2009

      47 Muto H, "Reduced TET2 function leads to T-cell lymphoma with follicular helper T-cell-like features in mice" 4 : e264-, 2014

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      49 Frauer C, "Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain" 6 : e21306-, 2011

      50 Hashimoto H, "Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation" 40 : 4841-4849, 2012

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      52 Kats LM, "Proto-oncogenic role of mutant IDH2 in leukemia initiation and maintenance" 14 : 329-341, 2014

      53 Iyer LM, "Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids" 8 : 1698-1710, 2009

      54 Bauer C, "Phosphorylation of TET proteins is regulated via O-GlcNAcylation by the O-linked N-acetylglucosamine transferase(OGT)" 290 : 4801-4812, 2015

      55 Brill LM, "Phosphoproteomic analysis of human embryonic stem cells" 5 : 204-213, 2009

      56 Andrews AJ, "Nucleosome structure(s) and stability: variations on a theme" 40 : 99-117, 2011

      57 Delhommeau F, "Mutation in TET2 in myeloid cancers" 360 : 2289-2301, 2009

      58 Wang L, "Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex" 523 : 621-625, 2015

      59 Ko M, "Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX" 497 : 122-126, 2013

      60 Gruenbaum Y, "Methylation of CpG sequences in eukaryotic DNA" 124 : 67-71, 1981

      61 Schiesser S, "Mechanism and stem-cell activity of 5-carboxycytosine decarboxylation determined by isotope tracing" 51 : 6516-6520, 2012

      62 Shen L, "Mechanism and function of oxidative reversal of DNA and RNA methylation" 83 : 585-614, 2014

      63 Mellen M, "MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system" 151 : 1417-1430, 2012

      64 Yildirim O, "Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells" 147 : 1498-1510, 2011

      65 Song CX, "Mapping recently identified nucleotide variants in the genome and transcriptome" 30 : 1107-1116, 2012

      66 Chen K, "Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer" 26 : 103-118, 2016

      67 Figueroa ME, "Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation" 18 : 553-567, 2010

      68 Ono R, "LCX, leukemia-associated protein with a CXXC domain, is fused to MLL in acute myeloid leukemia with trilineage dysplasia having t(10;11)(q22;q23)" 62 : 4075-4080, 2002

      69 Ko M, "Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2" 468 : 839-843, 2010

      70 Sasaki M, "IDH1(R132H) mutation increases murine haematopoietic progenitors and alters epigenetics" 488 : 656-659, 2012

      71 Ruiz MA, "Hydroxymethylcytosine and demethylation of the gamma-globin gene promoter during erythroid differentiation" 10 : 397-407, 2015

      72 Madzo J, "Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis" 6 : 231-244, 2014

      73 Guo JU, "Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain" 145 : 423-434, 2011

      74 Lister R, "Human DNA methylomes at base resolution show widespread epigenomic differences" 462 : 315-322, 2009

      75 Shearstone JR, "Global DNA demethylation during mouse erythropoiesis in vivo" 334 : 799-802, 2011

      76 Song CX, "Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming" 153 : 678-691, 2013

      77 Shen L, "Genome-wide analysis reveals TET-and TDG-dependent 5-methylcytosine oxidation dynamics" 153 : 692-706, 2013

      78 Meissner A, "Genome-scale DNA methylation maps of pluripotent and differentiated cells" 454 : 766-770, 2008

      79 Herman JG, "Gene silencing in cancer in association with promoter hypermethylation" 349 : 2042-2054, 2003

      80 한재아, "Functions of TET Proteins in Hematopoietic Transformation" 한국분자세포생물학회 38 (38): 925-935, 2015

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      84 Iacobuzio-Donahue CA, "Epigenetic changes in cancer" 4 : 229-249, 2009

      85 Valinluck V, "Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1" 67 : 946-950, 2007

      86 Cortázar D, "Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability" 470 : 419-423, 2011

      87 Ji D, "Effects of Tet-induced oxidation products of 5-methylcytosine on Dnmt1-and DNMT3a-mediated cytosine methylation" 10 : 1749-1752, 2014

      88 Spruijt CG, "Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives" 152 : 1146-1159, 2013

      89 Wu H, "Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells" 473 : 389-393, 2011

      90 Challen GA, "Dnmt3a is essential for hematopoietic stem cell differentiation" 44 : 23-31, 2012

      91 Huang Y, "Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells" 111 : 1361-1366, 2014

      92 Stadler MB, "DNA-binding factors shape the mouse methylome at distal regulatory regions" 480 : 490-495, 2011

      93 Bock C, "DNA methylation dynamics during in vivo differentiation of blood and skin stem cells" 47 : 633-647, 2012

      94 Ko M, "DNA methylation and hydroxymethylation in hematologic differentiation and transformation" 37 : 91-101, 2015

      95 Smith ZD, "DNA methylation : roles in mammalian development" 14 : 204-220, 2013

      96 Liutkeviciute Z, "Cytosine-5-methyltransferases add aldehydes to DNA" 5 : 400-402, 2009

      97 Hu L, "Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation" 155 : 1545-1555, 2013

      98 Xiong J, "Cooperative action between SALL4A and TET proteins in stepwise oxidation of 5-methylcytosine" 64 : 913-925, 2016

      99 Tahiliani M, "Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1" 324 : 930-935, 2009

      100 Huang Y, "Connections between TET proteins and aberrant DNA modification in cancer" 30 : 464-474, 2014

      101 Ji H, "Comprehensive methylome map of lineage commitment from haematopoietic progenitors" 467 : 338-342, 2010

      102 Zhao Z, "Combined loss of Tet1 and Tet2 promotes B cell, but not myeloid malignancies, in mice" 13 : 1692-1704, 2015

      103 Eden A, "Chromosomal instability and tumors promoted by DNA hypomethylation" 300 : 455-, 2003

      104 Wu H, "Charting oxidized methylcytosines at base resolution" 22 : 656-661, 2015

      105 Ziller MJ, "Charting a dynamic DNA methylation landscape of the human genome" 500 : 477-481, 2013

      106 Otani J, "Cell cycle-dependent turnover of 5-hydroxymethyl cytosine in mouse embryonic stem cells" 8 : E82961-, 2013

      107 Chen C, "Cancerassociated IDH2 mutants drive an acute myeloid leukemia that is susceptible to Brd4 inhibition" 27 : 1974-1985, 2013

      108 Dang L, "Cancer-associated IDH1 mutations produce 2-hydroxyglutarate" 465 : 966-, 2010

      109 Nakagawa T, "CRL4(VprBP)E3 ligase promotes monoubiquitylation and chromatin binding of TET dioxygenases" 57 : 247-260, 2015

      110 Xia B, "Bisulfite-free, baseresolution analysis of 5-formylcytosine at the genome scale" 12 : 1047-1050, 2015

      111 Yu M, "Baseresolution analysis of 5-hydroxymethylcytosine in the mammalian genome" 149 : 1368-1380, 2012

      112 Lu X, "Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics" 25 : 386-389, 2015

      113 Yin R, "Ascorbic acid enhances Tet-mediated 5-methylcytosine oxidation and promotes DNA demethylation in mammals" 135 : 10396-10403, 2013

      114 Minor EA, "Ascorbate induces ten-eleven translocation(Tet)methylcytosine dioxygenase-mediated generation of 5-hydroxymethylcytosine" 288 : 13669-13674, 2013

      115 Rohle D, "An inhibitor of mutant IDH1 delays growth and promotes differentiation of glioma cells" 340 : 626-630, 2013

      116 Iyer LM, "Adenine methylation in eukaryotes : Apprehending the complex evolutionary history and functional potential of an epigenetic modification" 38 : 27-40, 2016

      117 An J, "Acute loss of TET function results in aggressive myeloid cancer in mice" 6 : 10071-, 2015

      118 Nabel CS, "AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation" 8 : 751-758, 2012

      119 Iurlaro M, "A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation" 14 : R119-, 2013

      120 Williams RT, "A density functional theory study on the kinetics and thermodynamics of N-glycosidic bond cleavage in 5-substituted 2′-deoxycytidines" 51 : 6458-6462, 2012

      121 Hon GC, "5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation" 56 : 286-297, 2014

      122 Kellinger MW, "5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription" 19 : 831-833, 2012

      123 Stroud H, "5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells" 12 : R54-, 2011

      124 Bachman M, "5-Hydroxymethylcytosine is a predominantly stable DNA modification" 6 : 1049-1055, 2014

      125 Raiber EA, "5-Formylcytosine alters the structure of the DNA double helix" 22 : 44-49, 2015

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