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Review

CG Methylation

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Pages 655-663 | Published online: 18 Dec 2012

References

  • Wyatt GR . Recognition and estimation of 5-methylcytosine in nucleic acids. Biochem. J.48(5) , 581–584 (1951).
  • Bird AP , SouthernEM. Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis. J. Mol. Biol.118(1) , 27–47 (1978).
  • Adams RL , McKayEL, CraigLM, BurdonRH. Methylation of mosquito DNA. Biochim. Biophys. Acta563(1) , 72–81 (1979).
  • Rae PM , SteeleRE. Absence of cytosine methylation at C-C-G-G and G-C-G-C sites in the rDNA coding regions and intervening sequences of Drosophila and the rDNA of other insects. Nucleic Acids Res.6(9) , 2987–2995 (1979).
  • Bird AP , TaggartMH. Variable patterns of total DNA and rDNA methylation in animals. Nucleic Acids Res.8(7) , 1485–1497 (1980).
  • Bird AP . DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res.8(7) , 1499–1504 (1980).
  • Cooper DN , TaggartMH, BirdAP. Unmethylated domains in vertebrate DNA. Nucleic Acids Res.11(3) , 647–658 (1983).
  • Bird A , TaggartM, FrommerM, MillerOJ, MacleodD. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell40(1) , 91–99 (1985).
  • Bird AP . CpG-rich islands and the function of DNA methylation. Nature321(6067) , 209–213 (1986).
  • Iguchi-Ariga SM , SchaffnerW. CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation. Genes Dev.3(5) , 612–619 (1989).
  • Tate PH , BirdAP. Effects of DNA methylation on DNA-binding proteins and gene expression. Curr. Opin. Genet. Dev.3(2) , 226–231 (1993).
  • Rozenberg JM , ShlyakhtenkoA, GlassKet al. All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues. BMC Genomics 9 , 67 (2008).
  • Rishi V , BhattacharyaP, ChatterjeeRet al. CpG methylation of half-CRE sequences creates C/EBPαbinding sites that activate some tissue-specific genes. Proc. Natl Acad. Sci. USA 107(47) , 20311–20316 (2010).
  • Wilks AF , CozensPJ, MattajIW, JostJP. Estrogen induces a demethylation at the 5´ end region of the chicken vitellogenin gene. Proc. Natl Acad. Sci. USA79(14) , 4252–4255 (1982).
  • Grainger RM , Hazard-LeonardsRM, SamahaF, HouganLM, LeskMR, ThomsenGH. Is hypomethylation linked to activation of δ-crystallin genes during lens development? Nature306(5938) , 88–91 (1983).
  • Kunnath L , LockerJ. Developmental changes in the methylation of the rat albumin and α-fetoprotein genes. EMBO J.2(3) , 317–324 (1983).
  • Meehan RR , LewisJD, McKayS, KleinerEL, BirdAP. Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs. Cell58(3) , 499–507 (1989).
  • Lewis JD , MeehanRR, HenzelWJet al. Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 69(6) , 905–914 (1992).
  • Jones PL , VeenstraGJ, WadePAet al. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat. Genet. 19(2) , 187–191 (1998).
  • Baylin SB , JonesPA. A decade of exploring the cancer epigenome – biological and translational implications. Nat. Rev. Cancer11(10) , 726–734 (2011).
  • Frommer M , McDonaldLE, MillarDSet al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl Acad. Sci. USA 89(5) , 1827–1831 (1992).
  • MacLeod D , CharltonJ, MullinsJ, BirdAP. Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev.8(19) , 2282–2292 (1994).
  • Down TA , RakyanVK, TurnerDJet al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol. 26(7) , 779–785 (2008).
  • Ball MP , LiJB, GaoYet al. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol. 27(4) , 361–368 (2009).
  • Taiwo O , WilsonGA, MorrisTet al. Methylome analysis using MeDIP-seq with low DNA concentrations. Nat. Protoc. 7(4) , 617–636 (2012).
  • Lister R , O‘MalleyRC, Tonti-FilippiniJet al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133(3) , 523–536 (2008).
  • Lister R , PelizzolaM, DowenRHet al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271) , 315–322 (2009).
  • Lister R , PelizzolaM, KidaYSet al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471(7336) , 68–73 (2011).
  • Meissner A , MikkelsenTS, GuHet al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454(7205) , 766–770 (2008).
  • Eckhardt F , LewinJ, CorteseRet al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38(12) , 1378–1385 (2006).
  • Weber M , HellmannI, StadlerMBet al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39(4) , 457–466 (2007).
  • Hansen KD , TimpW, BravoHCet al. Increased methylation variation in epigenetic domains across cancer types. Nat. Genet. 43(8) , 768–775 (2011).
  • Elder JT , ZhaoX. Evidence for local control of gene expression in the epidermal differentiation complex. Exp. Dermatol.11(5) , 406–412 (2002).
  • Serman L , DodigD. Impact of DNA methylation on trophoblast function. Clin. Epigenetics3 , 7 (2011).
  • Botchkarev VA , GdulaMR, MardaryevAN, SharovAA, FessingMY. Epigenetic regulation of gene expression in keratinocytes. J. Invest. Dermatol.132(11) , 2505–2521 (2012).
  • Olszak T , AnD, ZeissigSet al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science 336(6080) , 489–493 (2012).
  • Deaton AM , BirdA. CpG islands and the regulation of transcription. Genes Dev.25(10) , 1010–1022 (2011).
  • Bird A . DNA methylation patterns and epigenetic memory. Genes Dev.16(1) , 6–21 (2002).
  • Saxonov S , BergP, BrutlagDL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl Acad. Sci. USA103(5) , 1412–1417 (2006).
  • Campanero MR , ArmstrongMI, FlemingtonEK. CpG methylation as a mechanism for the regulation of E2F activity. Proc. Natl Acad. Sci. USA97(12) , 6481–6486 (2000).
  • Sigurdsson MI , SmithAV, BjornssonHT, JonssonJJ. HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination. Genome Res.19(4) , 581–589 (2009).
  • Laurent L , WongE, LiGet al. Dynamic changes in the human methylome during differentiation. Genome Res. 20(3) , 320–331 (2010).
  • Reik W , DeanW, WalterJ. Epigenetic reprogramming in mammalian development. Science293(5532) , 1089–1093 (2001).
  • Rougier N , Bourc‘hisD, GomesDMet al. Chromosome methylation patterns during mammalian preimplantation development. Genes Dev. 12(14) , 2108–2113 (1998).
  • Mayer W , NiveleauA, WalterJ, FundeleR, HaafT. Demethylation of the zygotic paternal genome. Nature403(6769) , 501–502 (2000).
  • Oswald J , EngemannS, LaneNet al. Active demethylation of the paternal genome in the mouse zygote. Curr. Biol. 10(8) , 475–478 (2000).
  • Carlson LL , PageAW, BestorTH. Properties and localization of DNA methyltransferase in preimplantation mouse embryos: implications for genomic imprinting. Genes Dev.6(12B) , 2536–2541 (1992).
  • Cardoso MC , LeonhardtH. DNA methyltransferase is actively retained in the cytoplasm during early development. J. Cell Biol.147(1) , 25–32 (1999).
  • Hajkova P , AncelinK, WaldmannTet al. Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature 452(7189) , 877–881 (2008).
  • Farthing CR , FiczG, NgRKet al. Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes. PLoS Genet. 4(6) , e1000116 (2008).
  • Straussman R , NejmanD, RobertsDet al. Developmental programming of CpG island methylation profiles in the human genome. Nat. Struct. Mol. Biol. 16(5) , 564–571 (2009).
  • 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).
  • Takizawa T , NakashimaK, NamihiraMet al. DNA methylation is a critical cell-intrinsic determinant of astrocyte differentiation in the fetal brain. Dev. Cell 1(6) , 749–758 (2001).
  • Tsumura A , HayakawaT, KumakiYet al. Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells 11(7) , 805–814 (2006).
  • Sen GL , ReuterJA, WebsterDE, ZhuL, KhavariPA. DNMT1 maintains progenitor function in self-renewing somatic tissue. Nature463(7280) , 563–567 (2010).
  • Zhu JK . Active DNA demethylation mediated by DNA glycosylases. Annu. Rev. Genet.43 , 143–166 (2009).
  • Ito S , D‘AlessioAC, TaranovaOV, HongK, SowersLC, ZhangY. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature466(7310) , 1129–1133 (2010).
  • Ito S , ShenL, DaiQet al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333(6047) , 1300–1303 (2011).
  • Wu H , D‘AlessioAC, ItoSet al. Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev. 25(7) , 679–684 (2011).
  • Cortellino S , XuJ, SannaiMet al. Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell 146(1) , 67–79 (2011).
  • Lapeyre JN , BeckerFF. 5-methylcytosine content of nuclear DNA during chemical hepatocarcinogenesis and in carcinomas which result. Biochem. Biophys. Res. Commun.87(3) , 698–705 (1979).
  • Feinberg AP , VogelsteinB. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature301(5895) , 89–92 (1983).
  • Feinberg AP , OhlssonR, HenikoffS. The epigenetic progenitor origin of human cancer. Nat. Rev. Genet.7(1) , 21–33 (2006).
  • Rodriguez-Paredes M , EstellerM. Cancer epigenetics reaches mainstream oncology. Nat. Med.17(3) , 330–339 (2011).
  • Roman-Gomez J , Jimenez-VelascoA, AgirreXet al. Promoter hypomethylation of the LINE-1 retrotransposable elements activates sense/antisense transcription and marks the progression of chronic myeloid leukemia. Oncogene 24(48) , 7213–7223 (2005).
  • Cui H , Cruz-CorreaM, GiardielloFMet al. Loss of IGF2 imprinting: a potential marker of colorectal cancer risk. Science 299(5613) , 1753–1755 (2003).
  • Feinberg AP . Imprinting of a genomic domain of 11p15 and loss of imprinting in cancer: an introduction. Cancer Res.59(Suppl. 7) , S1743–S1746 (1999).
  • Ogawa O , EcclesMR, SzetoJet al. Relaxation of insulin-like growth factor II gene imprinting implicated in Wilms‘ tumour. Nature 362(6422) , 749–751 (1993).
  • Kaneda A , FeinbergAP. Loss of imprinting of IGF2: a common epigenetic modifier of intestinal tumor risk. Cancer Res.65(24) , 11236–11240 (2005).
  • Kriaucionis S , HeintzN. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science324(5929) , 929–930 (2009).
  • Tahiliani M , KohKP, ShenYet al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324(5929) , 930–935 (2009).
  • Ko M , HuangY, JankowskaAMet al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 468(7325) , 839–843 (2010).
  • Dawlaty MM , GanzK, PowellBEet al. Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development. Cell Stem Cell 9(2) , 166–175 (2011).
  • Gu TP , GuoF, YangHet al. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 477(7366) , 606–610 (2011).
  • Koh KP , YabuuchiA, RaoSet al. Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 8(2) , 200–213 (2011).
  • Szulwach KE , LiX, LiYet al. Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet. 7(6) , e1002154 (2011).
  • Yu M , HonGC, SzulwachKEet al. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149(6) , 1368–1380 (2012).
  • McDonald OG , WuH, TimpW, DoiA, FeinbergAP. Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition. Nat. Struct. Mol. Biol.18(8) , 867–874 (2011).
  • Bulyk ML , GentalenE, LockhartDJ, ChurchGM. Quantifying DNA–protein interactions by double-stranded DNA arrays. Nat. Biotechnol.17(6) , 573–577 (1999).
  • Warren CL , ZhaoJ, GlassK, RishiV, AnsariAZ, VinsonC. Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine. Lab Chip12(2) , 376–380 (2012).

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