DNA methylation: TET proteins-guardians of CpG islands?

EMBO Reports

Volumn 13, Issue 1, 2012, Pages 28-35

  Williams, Kristine ^a   Christensen, Jesper ^a   Helin, Kristian ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

5 hydroxymethylcytosine; cancer; DNA methylation; stem cells; TET proteins

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; DNA BINDING PROTEIN; PROTEIN TET; PROTEIN TET1; PROTEIN TET2; PROTEIN TET3; UNCLASSIFIED DRUG;

CPG ISLAND; DNA METHYLATION; EMBRYONIC STEM CELL; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; REVIEW; TRANSCRIPTION REGULATION;

5-METHYLCYTOSINE; ANIMALS; CPG ISLANDS; CYTOSINE; DNA METHYLATION; DNA-BINDING PROTEINS; EMBRYONIC STEM CELLS; GENE EXPRESSION REGULATION; HUMANS; MICE; PROTO-ONCOGENE PROTEINS; TRANSCRIPTION, GENETIC;

EID: 84555189745     PISSN: 1469221X     EISSN: 14693178     Source Type: Journal    
DOI: 10.1038/embor.2011.233     Document Type: Review

References (54)

1. Blackledge NP, Klose R (2011) CpG island chromatin: a platform for gene regulation. Epigenetics 6: 147-152
2. Bogdanovic O, Veenstra GJ (2009) DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Chromosoma 118: 549-565
3. Bostick M, Kim JK, Esteve PO, Clark A, Pradhan S, Jacobsen SE (2007) UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317: 1760-1764 (Pubitemid 47461842)
4. Cortellino S et al (2011) Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell 146: 67-79
5. Dawlaty MM et al (2011) Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development. Cell Stem Cell 9: 166-175
6. Deaton AM, Bird A (2011) CpG islands and the regulation of transcription. Genes Dev 25: 1010-1022
7. Delhommeau F et al (2009) Mutation in TET2 in myeloid cancers. N Engl J Med 360: 2289-2301
8. Feinberg AP, Ohlsson R, Henikoff S (2006) The epigenetic progenitor origin of human cancer. Nat Rev Genet 7: 21-33 (Pubitemid 41828945)
9. Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, Marques CJ, Andrews S, Reik W (2011) Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473: 398-402
10. Figueroa ME et al (2010) Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18: 553-567
11. Fouse SD, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, Fan G (2008) Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell 2: 160-169 (Pubitemid 351168712)
12. Globisch D, Munzel M, Muller M, Michalakis S, Wagner M, Koch S, Bruckl T, Biel M, Carell T (2010) Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS ONE 5: e15367
13. Goll MG, Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74: 481-514 (Pubitemid 40995515)
14. Guo JU, Su Y, Zhong C, Ming GL, Song H (2011) Emerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation and beyond. Cell Cycle 10: 2662-2668
15. He YF et al (2011) Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333: 1303-1307
16. Ito S, D'Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y (2010) Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466: 1129-1133
17. Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, He C, Zhang Y (2011) Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333: 1300-1303
18. Jankowska AM, Szpurka H, Tiu RV, Makishima H, Afable M, Huh J, O'Keefe CL, Ganetzky R, McDevitt MA, Maciejewski JP (2009) Loss of heterozygosity 4q24 and TET2 mutations associated with myelodysplastic/myeloproliferative neoplasms. Blood 113: 6403-6410
19. Jin SG, Kadam S, Pfeifer GP (2010) Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res 38: e125
20. Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128: 683-692 (Pubitemid 46273572)
21. Ko M et al (2010) Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 468: 839-843
22. Ko M, Bandukwala HS, An J, Lamperti ED, Thompson EC, Hastie R, Tsangaratou A, Rajewsky K, Koralov SB, Rao A (2011) Ten-eleven-translocation 2 (TET2) negatively regulates homeostasis and differentiation of hematopoietic stem cells in mice. Proc Natl Acad Sci USA 108: 14566-14571
23. Koh KP et al (2011) Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 8: 200-213
24. Kriaucionis S, Heintz N (2009) The nuclear DNA base 5- hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324: 929-930
25. Langemeijer SM et al (2009) Acquired mutations in TET2 are common in myelodysplastic syndromes. Nat Genet 41: 838-842
26. Li E, Bestor TH, Jaenisch R (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69: 915-926
27. Li Y et al (2010) The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol 8: e1000533
28. Li Z, Cai X, Cai C, Wang J, Zhang W, Petersen BE, Yang FC, Xu M (2011) Deletion of Tet2 in mice leads to dysregulated hematopoietic stem cells and subsequent development of myeloid malignancies. Blood 118: 4509-4518
29. Lister R et al (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322
30. Meissner A et al (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454: 766-770
31. Mikkelsen TS et al (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560 (Pubitemid 47206934)
32. Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB, Bibel M, Schubeler D (2008) Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol Cell 30: 755-766
33. Moran-Crusio K et al (2011) Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation. Cancer Cell 20: 11-24
34. Okano M, Bell DW, Haber DA, Li E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99: 247-257 (Pubitemid 29519904)
35. Ooi SK et al (2007) DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448: 714-717 (Pubitemid 47236857)
36. Otani J, Nankumo T, Arita K, Inamoto S, Ariyoshi M, Shirakawa M (2009) Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain. EMBO Rep 10: 1235-1241
37. Pastor WA et al (2011) Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473: 394-397
38. Pfaffeneder T, Hackner B, Truss M, Munzel M, Muller M, Deiml CA, Hagemeier C, Carell T (2011) The discovery of 5-formylcytosine in embryonic stem cell DNA. Angew Chem Int Ed Engl 50: 7008-7012
39. Quivoron C et al (2011) TET2 inactivation results in pleiotropic hematopoietic abnormalities in mouse and is a recurrent event during human lymphomagenesis. Cancer Cell 20: 25-38
40. Reik W, Dean W, Walter J (2001) Epigenetic reprogramming in mammalian development. Science 293: 1089-1093 (Pubitemid 32758081)
41. Sharif J et al (2007) The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 450: 908-912 (Pubitemid 350231331)
42. Szwagierczak A, Bultmann S, Schmidt CS, Spada F, Leonhardt H (2010) Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res 38: e181
43. Tahiliani M et al (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324: 930-935
44. Tsumura A et al (2006) Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells 11: 805-814 (Pubitemid 43923351)
45. Valinluck V, Sowers LC (2007) Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1. Cancer Res 67: 946-950
46. Valinluck V, Tsai HH, Rogstad DK, Burdzy A, Bird A, Sowers LC (2004) Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res 32: 4100-4108 (Pubitemid 39232282)
47. Weber M, Schubeler D (2007) Genomic patterns of DNA methylation: targets and function of an epigenetic mark. Curr Opin Cell Biol 19: 273-280 (Pubitemid 46899512)
48. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39: 457-466 (Pubitemid 46514772)
49. Williams K, Christensen J, Pedersen MT, Johansen J V, Cloos PA, Rappsilber J, Helin K (2011) TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 473: 343-348
50. Wu H, Zhang Y (2011) Tet1 and 5-hydroxymethylation: A genome-wide view in mouse embryonic stem cells. Cell Cycle 10: 2428-2436
51. Wu H, D'Alessio AC, Ito S, Xia K, Wang Z, Cui K, Zhao K, Sun YE, Zhang Y (2011a) Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 473: 389-393
52. Wu H, D'Alessio AC, Ito S, Wang Z, Cui K, Zhao K, Sun YE, Zhang Y (2011b) Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev 25: 679-684
53. Xu Y et al (2011) Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol Cell 42: 451-464
54. Zhang H, Zhang X, Clark E, Mulcahey M, Huang S, Shi YG (2010) TET1 is a DNA-binding protein that modulates DNA methylation and gene transcription via hydroxylation of 5-methylcytosine. Cell Res 20: 1390-1393