Potential functional roles of DNA demethylation intermediates

Trends in Biochemical Sciences

Volumn 38, Issue 10, 2013, Pages 480-484

  Song, Chun Xiao ^a   He, Chuan ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

5 carboxylcytosine; 5 formylcytosine; 5 hydroxymethylcytosine; Demethylation intermediates; Regulatory roles

Indexed keywords

5 CARBOXYLCYTOSINE; 5 FORMYLCYTOSINE; 5 HYDROXYMETHYLCYSOTINE; 5 METHYLCYTOSINE; CYTOSINE DERIVATIVE; DNA METHYLTRANSFERASE; THYMINE DNA GLYCOSYLASE; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

CELL DIFFERENTIATION; CELL MATURATION; CHROMATIN STRUCTURE; DEMETHYLATION; DNA METHYLATION; DNA MODIFICATION; EPIGENETICS; EXCISION REPAIR; GENE EXPRESSION; GENE MAPPING; GENETIC ASSOCIATION; HISTONE MODIFICATION; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; REGULATORY MECHANISM; REVIEW; TRANSCRIPTION REGULATION;

MAMMALIA;

5-CARBOXYLCYTOSINE; 5-FORMYLCYTOSINE; 5-HYDROXYMETHYLCYTOSINE; DEMETHYLATION INTERMEDIATES; REGULATORY ROLES;

5-METHYLCYTOSINE; DNA; DNA METHYLATION;

EID: 84884590688     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibs.2013.07.003     Document Type: Review

References (52)

1. Klose R.J., Bird A.P. Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci. 2006, 31:89-97.
2. Smith Z.D., Meissner A. DNA methylation: roles in mammalian development. Nat. Rev. Genet. 2013, 14:204-220.
3. Baylin S.B., Jones P.A. A decade of exploring the cancer epigenome - biological and translational implications. Nat. Rev. Cancer 2011, 11:726-734.
4. Wu S.C., Zhang Y. Active DNA demethylation: many roads lead to Rome. Nat. Rev. Mol. Cell Biol. 2010, 11:607-620.
5. Bhutani N., et al. DNA demethylation dynamics. Cell 2011, 146:866-872.
6. Kriaucionis S., Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009, 324:929-930.
7. Tahiliani M., et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009, 324:930-935.
8. Ito S., et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011, 333:1300-1303.
9. He Y.F., et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 2011, 333:1303-1307.
10. Wossidlo M., et al. 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nat. Commun. 2011, 2:241.
11. Iqbal K., et al. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:3642-3647.
12. Gu T.P., et al. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 2011, 477:606-610.
13. Inoue A., et al. Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development. Cell Res. 2011, 21:1670-1676.
14. Inoue A., Zhang Y. Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science 2011, 334:194.
15. Seisenberger S., et al. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol. Cell 2012, 48:849-862.
16. Yamaguchi S., et al. Tet1 controls meiosis by regulating meiotic gene expression. Nature 2012, 492:443-447.
17. Hackett J.A., et al. Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine. Science 2013, 339:448-452.
18. Vincent J.J., et al. Stage-specific roles for tet1 and tet2 in DNA demethylation in primordial germ cells. Cell Stem Cell 2013, 12:470-478.
19. Maiti A., Drohat A.C. Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites. J. Biol. Chem. 2011, 286:35334-35338.
20. Hackett J.A., et al. Parallel mechanisms of epigenetic reprogramming in the germline. Trends Genet. 2012, 28:164-174.
21. Guibert S., Weber M. Functions of DNA methylation and hydroxymethylation in mammalian development. Curr. Top. Dev. Biol. 2013, 104:47-83.
22. Guo J.U., et al. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 2011, 145:423-434.
23. Schiesser S., et al. Mechanism and stem-cell activity of 5-carboxycytosine decarboxylation determined by isotope tracing. Angew. Chem. Int. Ed. Engl. 2012, 51:6516-6520.
24. Raiber E.A., et al. Genome-wide distribution of 5-formylcytosine in ES cells is associated with transcription and depends on thymine DNA glycosylase. Genome Biol. 2012, 13:R69.
25. Song C.X., et al. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell 2013, 153:678-691.
26. Shen L., et al. Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics. Cell 2013, 153:692-706.
27. Zhu J.K. Active DNA demethylation mediated by DNA glycosylases. Annu. Rev. Genet. 2009, 43:143-166.
28. Jones P.A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 2012, 13:484-492.
29. Koh K.P., Rao A. DNA methylation and methylcytosine oxidation in cell fate decisions. Curr. Opin. Cell Biol. 2013, 25:152-161.
30. Shen L., Zhang Y. 5-Hydroxymethylcytosine: generation, fate, and genomic distribution. Curr. Opin. Cell Biol. 2013, 25:289-296.
31. Stadler M.B., et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 2011, 480:490-495.
32. Yu M., et al. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 2012, 149:1368-1380.
33. Song C.X., et al. Mapping recently identified nucleotide variants in the genome and transcriptome. Nat. Biotechnol. 2012, 30:1107-1116.
34. Song C.X., et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat. Biotechnol. 2011, 29:68-72.
35. Mellen M., et al. MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell 2012, 151:1417-1430.
36. Szulwach K.E., et al. 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat. Neurosci. 2011, 14:1607-1616.
37. Hahn M.A., et al. Dynamics of 5-hydroxymethylcytosine and chromatin marks in Mammalian neurogenesis. Cell Rep. 2013, 3:291-300.
38. Gao Y., et al. Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA methylation and hydroxymethylation in reprogramming. Cell Stem Cell 2013, 12:453-469.
39. Jin S-G., et al. 5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations. Cancer Res. 2011, 71:7360-7365.
40. Doege C.A., et al. Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2. Nature 2012, 488:652-655.
41. Costa Y., et al. NANOG-dependent function of TET1 and TET2 in establishment of pluripotency. Nature 2013, 495:370-374.
42. Piccolo F.M., et al. Different roles for Tet1 and Tet2 proteins in reprogramming-mediated erasure of imprints induced by EGC fusion. Mol. Cell 2013, 49:1023-1033.
43. Cantone I., Fisher A.G. Epigenetic programming and reprogramming during development. Nat. Struct. Mol. Biol. 2013, 20:282-289.
44. Yildirim O., et al. Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell 2011, 147:1498-1510.
45. Spruijt C.G., et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 2013, 152:1146-1159.
46. Pfaffeneder T., et al. The discovery of 5-formylcytosine in embryonic stem cell DNA. Angew. Chem. Int. Ed. Engl. 2011, 50:7008-7012.
47. Booth M.J., et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 2012, 336:934-937.
48. Williams K., et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011, 473:343-348.
49. Wu H., et al. Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 2011, 473:389-393.
50. Hu J., et al. Selective chemical labelling of 5-formylcytosine in DNA by fluorescent dyes. Chemistry 2013, 19:5836-5840.
51. Kellinger M.W., et al. 5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 2012, 19:831-833.
52. Chen J., Li Q. Life and death of transcriptional co-activator p300. Epigenetics 2011, 6:957-961.