Biological and Biochemical Modulation of DNA Methylation

References

• Fournier A , SasaiN , NakaoM , DefossezPA . The role of methyl-binding proteins in chromatin organization and epigenome maintenance . Brief. Funct. Genomics11 ( 3 ), 251 – 264 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Cooper DN , KrawczakM . Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes . Hum. Genet.83 ( 2 ), 181 – 188 ( 1989 ).
   PubMed Web of Science ®Google Scholar
• Robertson KD , JonesPA . DNA methylation: past, present and future directions . Carcinogenesis21 ( 3 ), 461 – 467 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Bird A . The essentials of DNA methylation . Cell70 ( 1 ), 5 – 8 ( 1992 ).
   PubMed Web of Science ®Google Scholar
• Okano M , BellDW , HaberDA , LiE . DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development . Cell99 ( 3 ), 247 – 257 ( 1999 ).
   PubMed Web of Science ®Google Scholar
• Pradhan S , BacollaA , WellsRD , RobertsRJ . Recombinant human DNA (cytosine-5) methyltransferase. I. Expression, purification, and comparison of de novo and maintenance methylation . J. Biol. Chem.274 ( 46 ), 33002 – 33010 ( 1999 ).
   PubMed Web of Science ®Google Scholar
• Rountree MR , BachmanKE , BaylinSB . DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci . Nat. Genet.25 ( 3 ), 269 – 277 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Fellinger K , RothbauerU , FelleM , LangstG , LeonhardtH . Dimerization of DNA methyltransferase 1 is mediated by its regulatory domain . J. Cell. Biochem.106 ( 4 ), 521 – 528 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Pradhan M , EstevePO , ChinHG , SamaranaykeM , KimGD , PradhanS . CXXC domain of human DNMT1 is essential for enzymatic activity . Biochemistry47 ( 38 ), 10000 – 10009 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Fatemi M , HermannA , PradhanS , JeltschA . The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA . J. Mol. Biol.309 ( 5 ), 1189 – 1199 ( 2001 ).
   PubMed Web of Science ®Google Scholar
• Margot JB , Ehrenhofer-MurrayAE , LeonhardtH . Interactions within the mammalian DNA methyltransferase family . BMC Mol. Biol.4 , 7 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Li E , BestorTH , JaenischR . Targeted mutation of the DNA methyltransferase gene results in embryonic lethality . Cell69 ( 6 ), 915 – 926 ( 1992 ).
   PubMed Web of Science ®Google Scholar
• Okano M , XieS , LiE . Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases . Nat. Genet.19 ( 3 ), 219 – 220 ( 1998 ).
   PubMed Web of Science ®Google Scholar
• Kaneda M , OkanoM , HataKet al. Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting . Nature429 ( 6994 ), 900 – 903 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Tatton-Brown K , SealS , RuarkEet al. Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability . Nat. Genet.46 ( 4 ), 385 – 388 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Hansen RS , WijmengaC , LuoPet al. The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome . Proc. Natl Acad. Sci. USA96 ( 25 ), 14412 – 14417 ( 1999 ).
   PubMed Web of Science ®Google Scholar
• Suetake I , MiyazakiJ , MurakamiC , TakeshimaH , TajimaS . Distinct enzymatic properties of recombinant mouse DNA methyltransferases Dnmt3a and Dnmt3b . J. Biochem.133 ( 6 ), 737 – 744 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Umehara Y , HanaokaK , WatanabeD . Distinct functions of Dnmt3a and Dnmt3b de novo DNA methyltransferase in ES cell proliferation and differentiation . Stem Cell Discov.3 , 127 – 132 ( 2013 ).
   Google Scholar
• Handa V , JeltschA . Profound flanking sequence preference of Dnmt3a and Dnmt3b mammalian DNA methyltransferases shape the human epigenome . J. Mol. Biol.348 ( 5 ), 1103 – 1112 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Aapola U , KawasakiK , ScottHSet al. Isolation and initial characterization of a novel zinc finger gene, DNMT3L, on 21q22.3, related to the cytosine-5-methyltransferase 3 gene family . Genomics65 ( 3 ), 293 – 298 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Kareta MS , BotelloZM , EnnisJJ , ChouC , ChedinF . Reconstitution and mechanism of the stimulation of de novo methylation by human DNMT3L . J. Biol. Chem.281 ( 36 ), 25893 – 25902 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Hata K , OkanoM , LeiH , LiE . Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice . Development129 ( 8 ), 1983 – 1993 ( 2002 ).
   PubMed Web of Science ®Google Scholar
• Bourc’his D , XuGL , LinCS , BollmanB , BestorTH . Dnmt3L and the establishment of maternal genomic imprints . Science294 ( 5551 ), 2536 – 2539 ( 2001 ).
   PubMed Web of Science ®Google Scholar
• Neri F , KrepelovaA , IncarnatoDet al. Dnmt3L antagonizes DNA methylation at bivalent promoters and favors DNA methylation at gene bodies in ESCs . Cell155 ( 1 ), 121 – 134 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Ooi SK , QiuC , BernsteinEet al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA . Nature448 ( 7154 ), 714 – 717 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Li W , LiuM . Distribution of 5-hydroxymethylcytosine in different human tissues . J. Nucleic Acids2011 , 870726 ( 2011 ).
   PubMedGoogle Scholar
• Song CX , SzulwachKE , FuYet al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine . Nat. Biotechnol.29 ( 1 ), 68 – 72 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Tahiliani M , KohKP , ShenYet al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1 . Science324 ( 5929 ), 930 – 935 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Pastor WA , PapeUJ , HuangYet al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells . Nature473 ( 7347 ), 394 – 397 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Stroud H , FengS , Morey KinneyS , PradhanS , JacobsenSE . 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells . Genome Biol.12 ( 6 ), R54 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Valinluck V , SowersLC . Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1 . Cancer Res.67 ( 3 ), 946 – 950 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Ito S , ShenL , DaiQet al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine . Science333 ( 6047 ), 1300 – 1303 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• He YF , LiBZ , LiZet al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA . Science333 ( 6047 ), 1303 – 1307 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Hashimoto H , HongS , BhagwatAS , ZhangX , ChengX . Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation . Nucleic Acids Res.40 ( 20 ), 10203 – 10214 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Tan M , LuoH , LeeSet al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification . Cell146 ( 6 ), 1016 – 1028 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Feldman N , GersonA , FangJet al. G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis . Nat. Cell Biol.8 ( 2 ), 188 – 194 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Epsztejn-Litman S , FeldmanN , Abu-RemailehMet al. De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes . Nat. Struct. Mol. Biol.15 ( 11 ), 1176 – 1183 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Schlesinger Y , StraussmanR , KeshetIet al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer . Nat. Genet.39 ( 2 ), 232 – 236 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Vire E , BrennerC , DeplusRet al. The Polycomb group protein EZH2 directly controls DNA methylation . Nature439 ( 7078 ), 871 – 874 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Grafodatskaya D , ChungBH , ButcherDTet al. Multilocus loss of DNA methylation in individuals with mutations in the histone H3 lysine 4 demethylase KDM5C . BMC Med. Genomics6 , 1 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Chen BF , GuS , SuenYK , LiL , ChanWY . microRNA-199a-3p, DNMT3A, and aberrant DNA methylation in testicular cancer . Epigenetics9 ( 1 ), 119 – 128 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Garzon R , LiuS , FabbriMet al. MicroRNA-29b induces global DNA hypomethylation and tumor suppressor gene reexpression in acute myeloid leukemia by targeting directly DNMT3A and 3B and indirectly DNMT1 . Blood113 ( 25 ), 6411 – 6418 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Pan W , ZhuS , YuanMet al. MicroRNA-21 and microRNA-148a contribute to DNA hypomethylation in lupus CD4+ T cells by directly and indirectly targeting DNA methyltransferase 1 . J. Immunol.184 ( 12 ), 6773 – 6781 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Di Ruscio A , EbralidzeAK , BenoukrafTet al. DNMT1-interacting RNAs block gene-specific DNA methylation . Nature503 ( 7476 ), 371 – 376 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Goffin J , EisenhauerE . DNA methyltransferase inhibitors-state of the art . Ann. Oncol.13 ( 11 ), 1699 – 1716 ( 2002 ).
   PubMed Web of Science ®Google Scholar
• Christman JK . 5-Azacytidine and 5-aza-2′-deoxycytidine as inhibitors of DNA methylation: mechanistic studies and their implications for cancer therapy . Oncogene21 ( 35 ), 5483 – 5495 ( 2002 ).
   PubMed Web of Science ®Google Scholar
• Lin KT , MomparlerRL , RivardGE . High-performance liquid chromatographic analysis of chemical stability of 5-aza-2′-deoxycytidine . J. Pharm. Sci.70 ( 11 ), 1228 – 1232 ( 1981 ).
   PubMed Web of Science ®Google Scholar
• Baylin SB , JonesPA . A decade of exploring the cancer epigenome – biological and translational implications . Nat. Rev. Cancer11 ( 10 ), 726 – 734 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Cheng JC , MatsenCB , GonzalesFAet al. Inhibition of DNA methylation and reactivation of silenced genes by zebularine . J. Natl Cancer Inst.95 ( 5 ), 399 – 409 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Davis AJ , GelmonKA , SiuLLet al. Phase I and pharmacologic study of the human DNA methyltransferase antisense oligodeoxynucleotide MG98 given as a 21-day continuous infusion every 4 weeks . Invest. New Drugs21 ( 1 ), 85 – 97 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Schirrmacher E , BeckC , BruecknerBet al. Synthesis and in vitro evaluation of biotinylated RG108: a high affinity compound for studying binding interactions with human DNA methyltransferases . Bioconjug. Chem.17 ( 2 ), 261 – 266 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Brueckner B , Garcia BoyR , SiedleckiPet al. Epigenetic reactivation of tumor suppressor genes by a novel small-molecule inhibitor of human DNA methyltransferases . Cancer Res.65 ( 14 ), 6305 – 6311 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Pina IC , GautschiJT , WangGYet al. Psammaplins from the sponge Pseudoceratina purpurea: inhibition of both histone deacetylase and DNA methyltransferase . J. Org. Chem.68 ( 10 ), 3866 – 3873 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Baud MG , LeiserT , HausPet al. Defining the mechanism of action and enzymatic selectivity of psammaplin A against its epigenetic targets . J. Med. Chem.55 ( 4 ), 1731 – 1750 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Trejo-Becerril C , Perez-CardenasE , Trevino-CuevasHet al. Circulating nucleosomes and response to chemotherapy: an in vitro, in vivo and clinical study on cervical cancer patients . Int. J. Cancer104 ( 6 ), 663 – 668 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Singh N , Duenas-GonzalezA , LykoF , Medina-FrancoJL . Molecular modeling and molecular dynamics studies of hydralazine with human DNA methyltransferase 1 . ChemMedChem4 ( 5 ), 792 – 799 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Lee WJ , ShimJY , ZhuBT . Mechanisms for the inhibition of DNA methyltransferases by tea catechins and bioflavonoids . Mol. Pharmacol.68 ( 4 ), 1018 – 1030 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Caudill MA , WangJC , MelnykSet al. Intracellular S-adenosylhomocysteine concentrations predict global DNA hypomethylation in tissues of methyl-deficient cystathionine beta-synthase heterozygous mice . J. Nutr.131 ( 11 ), 2811 – 2818 ( 2001 ).
   PubMed Web of Science ®Google Scholar
• Lee BH , YegnasubramanianS , LinX , NelsonWG . Procainamide is a specific inhibitor of DNA methyltransferase 1 . J. Biol Chem.280 ( 49 ), 40749 – 40756 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Kuck D , CaulfieldT , LykoF , Medina-FrancoJL . Nanaomycin A selectively inhibits DNMT3B and reactivates silenced tumor suppressor genes in human cancer cells . Mol. Cancer Ther.9 ( 11 ), 3015 – 3023 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Gorelik G , RichardsonB . Key role of ERK pathway signaling in lupus . Autoimmunity43 ( 1 ), 17 – 22 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Zhao M , LiangG , WuXet al. Abnormal epigenetic modifications in peripheral blood mononuclear cells from patients with alopecia areata . Br. J. Dermatol.166 ( 2 ), 226 – 273 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Koppelman GH , NawijnMC . Recent advances in the epigenetics and genomics of asthma . Curr. Opin Allergy Clin. Immunol.11 ( 5 ), 414 – 419 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Baccarelli A , RienstraM , BenjaminEJ . Cardiovascular epigenetics: basic concepts and results from animal and human studies . Circulation3 ( 6 ), 567 – 573 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Tsai CN , TsaiCL , TseKP , ChangHY , ChangYS . The Epstein-Barr virus oncogene product, latent membrane protein 1, induces the downregulation of E-cadherin gene expression via activation of DNA methyltransferases . Proc. Natl Acad. Sci. USA99 ( 15 ), 10084 – 10089 ( 2002 ).
   PubMed Web of Science ®Google Scholar
• Okamoto Y , ShinjoK , ShimizuYet al. Hepatitis virus infection affects DNA methylation in mice with humanized livers . Gastroenterology146 ( 2 ), 562 – 572 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Maekita T , NakazawaK , MiharaMet al. High levels of aberrant DNA methylation in Helicobacter pylori-infected gastric mucosae and its possible association with gastric cancer risk . Clin. Cancer Res.12 ( 3 Pt 1 ), 989 – 995 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Niwa T , TsukamotoT , ToyodaTet al. Inflammatory processes triggered by Helicobacter pylori infection cause aberrant DNA methylation in gastric epithelial cells . Cancer Res.70 ( 4 ), 1430 – 1440 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Bednarik DP , DuckettC , KimSUet al. DNA CpG methylation inhibits binding of NF-kappa B proteins to the HIV-1 long terminal repeat cognate DNA motifs . New Biol.3 ( 10 ), 969 – 976 ( 1991 ).
   PubMedGoogle Scholar
• Smith GM , WhelanJ , PesciniR , GhersaP , DelamarterJF , Hooft Van HuijsduijnenR . DNA-methylation of the E-selectin promoter represses NF-kappa B transactivation . Biochem. Biophys. Res. Commun.194 ( 1 ), 215 – 221 ( 1993 ).
   PubMed Web of Science ®Google Scholar
• Fu LH , MaCL , CongB , LiSJ , ChenHY , ZhangJG . Hypomethylation of proximal CpG motif of interleukin-10 promoter regulates its expression in human rheumatoid arthritis . Acta Pharmacol. Sin.32 ( 11 ), 1373 – 1380 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Bruniquel D , SchwartzRH . Selective, stable demethylation of the interleukin-2 gene enhances transcription by an active process . Nat. Immunol.4 ( 3 ), 235 – 240 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Sullivan KE , ReddyAB , DietzmannKet al. Epigenetic regulation of tumor necrosis factor alpha . Mol. Cell Biol.27 ( 14 ), 5147 – 5160 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Foran E , Garrity-ParkMM , MureauCet al. Upregulation of DNA methyltransferase-mediated gene silencing, anchorage-independent growth, and migration of colon cancer cells by interleukin-6 . Mol. Cancer Res.8 ( 4 ), 471 – 481 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Li Y , DeuringJ , PeppelenboschMP , KuipersEJ , De HaarC , Van Der WoudeCJ . IL-6-induced DNMT1 activity mediates SOCS3 promoter hypermethylation in ulcerative colitis-related colorectal cancer . Carcinogenesis33 ( 10 ), 1889 – 1896 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Chen BF , ChanWY . The de novo DNA methyltransferase DNMT3A in development and cancer . Epigenetics9 ( 5 ), 669 – 677 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Klein CJ , BotuyanMV , WuYet al. Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss . Nat. Genet.43 ( 6 ), 595 – 600 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Margot JB , Aguirre-ArtetaAM , Di GiaccoBVet al. Structure and function of the mouse DNA methyltransferase gene: Dnmt1 shows a tripartite structure . J. Mol. Biol.297 ( 2 ), 293 – 300 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Wright A , DyckPJ . Hereditary sensory neuropathy with sensorineural deafness and early-onset dementia . Neurology45 ( 3 Pt 1 ), 560 – 562 ( 1995 ).
   PubMed Web of Science ®Google Scholar
• Winkelmann J , LinL , SchormairBet al. Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy . Hum. Mol. Genet.21 ( 10 ), 2205 – 2210 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Gaidzik VI , SchlenkRF , PaschkaPet al. Clinical impact of DNMT3A mutations in younger adult patients with acute myeloid leukemia: results of the AML Study Group (AMLSG) . Blood121 ( 23 ), 4769 – 4777 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Ribeiro AF , PratcoronaM , Erpelinck-VerschuerenCet al. Mutant DNMT3A. a marker of poor prognosis in acute myeloid leukemia . Blood119 ( 24 ), 5824 – 5831 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Thiede C . Mutant DNMT3A. teaming up to transform . Blood119 ( 24 ), 5615 – 5617 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Hagleitner MM , LankesterA , MaraschioPet al. Clinical spectrum of immunodeficiency, centromeric instability and facial dysmorphism (ICF syndrome) . J. Med. Genet.45 ( 2 ), 93 – 99 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Ko M , HuangY , JankowskaAMet al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2 . Nature468 ( 7325 ), 839 – 843 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Liu WJ , TanXH , LuoXPet al. Prognostic significance of TET2 mutations in adult patients with acute myeloid leukemia: a meta-analysis . Leuk. Lymphoma doi:10.3109/10428194.2014.893308 ( Epub ahead of print ) ( 2014 ).
   Google Scholar
• Gaidzik VI , PaschkaP , SpathDet al. TET2 mutations in acute myeloid leukemia (AML): results from a comprehensive genetic and clinical analysis of the AML study group . J. Clin. Oncol.30 ( 12 ), 1350 – 1357 ( 2012 ).
   PubMed Web of Science ®Google Scholar