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Charting oxidized methylcytosines at base resolution

Nature Structural & Molecular Biology volume 22, pages 656–661 (2015)Cite this article

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Abstract

DNA cytosine methylation is a key epigenetic mark that is required for normal mammalian development. Iterative oxidation of 5-methylcytosine (5mC) by the TET family of DNA dioxygenases generates three oxidized nucleotides: 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Recent advances in genomic mapping techniques have suggested that these oxidized cytosines not only function in the process of active reversal of 5mC but also may possess unique regulatory functions in the mammalian genome.

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Figure 1: Schematic diagram of potential functions for 5hmC, 5fC and 5caC.
Figure 2: Schematic diagram of base-resolution mapping methods for 5hmC, 5fC and 5caC.

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References

  1. Arber, W. & Dussoix, D. Host specificity of DNA produced by Escherichia coli. I. Host controlled modification of bacteriophage lambda. J. Mol. Biol. 5, 18–36 (1962).

    Article  CAS  PubMed  Google Scholar 

  2. Law, J.A. & Jacobsen, S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Greer, E.L. et al. DNA methylation on N6-adenine in C. elegans. Cell 161, 868–878 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Zhang, G. et al. N6-methyladenine DNA modification in Drosophila. Cell 161, 893–906 (2015).

    Article  CAS  PubMed  Google Scholar 

  5. Suzuki, M.M. & Bird, A. DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet. 9, 465–476 (2008).

    Article  CAS  PubMed  Google Scholar 

  6. Schübeler, D. Function and information content of DNA methylation. Nature 517, 321–326 (2015).

    Article  PubMed  CAS  Google Scholar 

  7. Bestor, T.H. The DNA methyltransferases of mammals. Hum. Mol. Genet. 9, 2395–2402 (2000).

    Article  CAS  PubMed  Google Scholar 

  8. Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002).

    Article  CAS  PubMed  Google Scholar 

  9. Reik, W., Dean, W. & Walter, J. Epigenetic reprogramming in mammalian development. Science 293, 1089–1093 (2001).

    Article  CAS  PubMed  Google Scholar 

  10. Wu, S.C. & Zhang, Y. Active DNA demethylation: many roads lead to Rome. Nat. Rev. Mol. Cell Biol. 11, 607–620 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Smith, Z.D. & Meissner, A. DNA methylation: roles in mammalian development. Nat. Rev. Genet. 14, 204–220 (2013).

    Article  CAS  PubMed  Google Scholar 

  12. Jones, P.A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 13, 484–492 (2012).

    Article  CAS  PubMed  Google Scholar 

  13. Wu, H. & Zhang, Y. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell 156, 45–68 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Pastor, W.A., Aravind, L. & Rao, A. TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat. Rev. Mol. Cell Biol. 14, 341–356 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Kriaucionis, S. & Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929–930 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Ito, S. et al. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466, 1129–1133 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. He, Y.F. et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333, 1303–1307 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Ito, S. et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300–1303 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. 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. 286, 35334–35338 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kohli, R.M. & Zhang, Y. TET enzymes, TDG and the dynamics of DNA demethylation. Nature 502, 472–479 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Spruijt, C.G. et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152, 1146–1159 (2013).

    Article  CAS  PubMed  Google Scholar 

  23. Iurlaro, M. et al. A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation. Genome Biol. 14, R119 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  24. 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. 19, 831–833 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Wang, L. et al. Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex. Nature 523, 621–625 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Raiber, E.A. et al. 5-Formylcytosine alters the structure of the DNA double helix. Nat. Struct. Mol. Biol. 22, 44–49 (2015).

    Article  CAS  PubMed  Google Scholar 

  27. Szulik, M.W. et al. Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Biochemistry 54, 1294–1305 (2015).

    Article  CAS  PubMed  Google Scholar 

  28. Song, C.X. & He, C. Potential functional roles of DNA demethylation intermediates. Trends Biochem. Sci. 38, 480–484 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Ko, M. et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 468, 839–843 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Bachman, M. et al. 5-Hydroxymethylcytosine is a predominantly stable DNA modification. Nat. Chem. 6, 1049–1055 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Shen, L. et al. Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics. Cell 153, 692–706 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Song, C.-X. et al. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell 153, 678–691 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Inoue, A., Shen, L., Dai, Q., He, C. & Zhang, Y. Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development. Cell Res. 21, 1670–1676 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Bachman, M. et al. 5-Formylcytosine can be a stable DNA modification in mammals. Nat. Chem. Biol. 11, 555–557 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Song, C.X., Yi, C. & He, C. Mapping recently identified nucleotide variants in the genome and transcriptome. Nat. Biotechnol. 30, 1107–1116 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Plongthongkum, N., Diep, D.H. & Zhang, K. Advances in the profiling of DNA modifications: cytosine methylation and beyond. Nat. Rev. Genet. 15, 647–661 (2014).

    Article  CAS  PubMed  Google Scholar 

  37. Booth, M.J., Raiber, E.A. & Balasubramanian, S. Chemical methods for decoding cytosine modifications in DNA. Chem. Rev. 115, 2240–2254 (2015).

    Article  CAS  PubMed  Google Scholar 

  38. Booth, M.J. et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336, 934–937 (2012).

    Article  CAS  PubMed  Google Scholar 

  39. Wu, H. et al. Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev. 25, 679–684 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Pastor, W.A. et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473, 394–397 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Yu, M. et al. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149, 1368–1380 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Stroud, H., Feng, S., Morey Kinney, S., Pradhan, S. & Jacobsen, S.E. 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol. 12, R54 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Szulwach, K.E. et al. Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet. 7, e1002154 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Szulwach, K.E. et al. 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat. Neurosci. 14, 1607–1616 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Lister, R. et al. Global epigenomic reconfiguration during mammalian brain development. Science 341, 1237905 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  46. Wang, L. et al. Programming and inheritance of parental DNA methylomes in mammals. Cell 157, 979–991 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Shen, L. et al. Tet3 and DNA replication mediate demethylation of both the maternal and paternal genomes in mouse zygotes. Cell Stem Cell 15, 459–470 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Guo, F. et al. Active and passive demethylation of male and female pronuclear DNA in the mammalian zygote. Cell Stem Cell 15, 447–458 (2014).

    Article  CAS  PubMed  Google Scholar 

  49. Sun, Z. et al. A sensitive approach to map genome-wide 5-hydroxymethylcytosine and 5-formylcytosine at single-base resolution. Mol. Cell 57, 750–761 (2015).

    Article  CAS  PubMed  Google Scholar 

  50. Song, C.X. et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat. Biotechnol. 29, 68–72 (2011).

    Article  CAS  PubMed  Google Scholar 

  51. Booth, M.J., Marsico, G., Bachman, M., Beraldi, D. & Balasubramanian, S. Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution. Nat. Chem. 6, 435–440 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Lu, X. et al. Chemical modification-assisted bisulfite sequencing (CAB-Seq) for 5-carboxylcytosine detection in DNA. J. Am. Chem. Soc. 135, 9315–9317 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Lu, X. et al. Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics. Cell Res. 25, 386–389 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Wu, H., Wu, X., Shen, L. & Zhang, Y. Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing. Nat. Biotechnol. 32, 1231–1240 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Neri, F. et al. Single-base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals promoter DNA methylation dynamics. Cell Rep. 10, 674–683 (2015).

    Article  CAS  PubMed  Google Scholar 

  56. Ooi, S.K. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Boulard, M., Edwards, J.R. & Bestor, T.H. FBXL10 protects Polycomb-bound genes from hypermethylation. Nat. Genet. 47, 479–485 (2015).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank L.M. Tuesta for critical reading of the manuscript. This work was supported by US National Institutes of Health grants GM68804 and U01DK089565 (to Y.Z.). H.W. was supported by a postdoctoral fellowship from the Jane Coffin Childs Memorial Fund for Medical Research and is currently supported by the US National Human Genome Research Institute (K99HG007982). Y.Z. is supported as an Investigator of the Howard Hughes Medical Institute.

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Authors and Affiliations

  1. Howard Hughes Medical Institute, Boston, Massachusetts, USA

    Hao Wu & Yi Zhang

  2. Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA

    Hao Wu & Yi Zhang

  3. Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA

    Hao Wu & Yi Zhang

  4. Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, USA

    Hao Wu & Yi Zhang

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Correspondence to Yi Zhang.

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Wu, H., Zhang, Y. Charting oxidized methylcytosines at base resolution. Nat Struct Mol Biol 22, 656–661 (2015). https://doi.org/10.1038/nsmb.3071

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