5-Formylcytosine alters the structure of the DNA double helix (original) (raw)

References

  1. Ito, S. et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300–1303 (2011).
    Article CAS Google Scholar
  2. Pfaffeneder, T. et al. The discovery of 5-formylcytosine in embryonic stem cell DNA. Angew. Chem. Int. Ed. Engl. 50, 7008–7012 (2011).
    Article CAS Google Scholar
  3. 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 Google Scholar
  4. Hashimoto, H., Hong, S., Bhagwat, A.S., Zhang, X. & Cheng, X. 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, 10203–10214 (2012).
    Article CAS Google Scholar
  5. 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 Google Scholar
  6. Renciuk, D., Blacque, O., Vorlickova, M. & Spingler, B. Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine. Nucleic Acids Res. 41, 9891–9900 (2013).
    Article CAS Google Scholar
  7. Lercher, L. et al. Structural insights into how 5-hydroxymethylation influences transcription factor binding. Chem. Commun. (Camb.) 50, 1794–1796 (2014).
    Article CAS Google Scholar
  8. Wang, L. et al. Programming and inheritance of parental DNA methylomes in mammals. Cell 157, 979–991 (2014).
    Article CAS Google Scholar
  9. Raiber, E.A. et al. Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase. Genome Biol. 13, R69 (2012).
    Article Google Scholar
  10. Song, C.X. et al. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell 153, 678–691 (2013).
    Article CAS Google Scholar
  11. Shen, L. et al. Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics. Cell 153, 692–706 (2013).
    Article CAS Google Scholar
  12. You, C. et al. Effects of Tet-mediated oxidation products of 5-methylcytosine on DNA transcription in vitro and in mammalian cells. Sci. Rep. 4, 7052 (2014).
    Article CAS Google Scholar
  13. Hu, L. et al. Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation. Cell 155, 1545–1555 (2013).
    Article CAS Google Scholar
  14. Xu, L. et al. Pyrene-based quantitative detection of the 5-formylcytosine loci symmetry in the CpG duplex content during TET-dependent demethylation. Angew. Chem. Int. Edn. Engl. 53, 11223–11227 (2014).
    Article CAS Google Scholar
  15. Thalhammer, A., Hansen, A.S., El-Sagheer, A.H., Brown, T. & Schofield, C.J. Hydroxylation of methylated CpG dinucleotides reverses stabilisation of DNA duplexes by cytosine 5-methylation. Chem. Commun. (Camb.) 47, 5325–5327 (2011).
    Article CAS Google Scholar
  16. Sutherland, J.C., Griffin, K.P., Keck, P.C. & Takacs, P.Z. Z-DNA: vacuum ultraviolet circular dichroism. Proc. Natl. Acad. Sci. USA 78, 4801–4804 (1981).
    Article CAS Google Scholar
  17. 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 Google Scholar
  18. Spruijt, C.G. et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152, 1146–1159 (2013).
    Article CAS Google Scholar
  19. Wyatt, M.D., Allan, J.M., Lau, A.Y., Ellenberger, T.E. & Samson, L.D. 3-methyladenine DNA glycosylases: structure, function, and biological importance. BioEssays 21, 668–676 (1999).
    Article CAS Google Scholar
  20. Kabsch, W. Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr. D Biol. Crystallogr. 66, 133–144 (2010).
    Article CAS Google Scholar
  21. Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
    Article CAS Google Scholar
  22. Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
    Article CAS Google Scholar
  23. Zheng, G., Lu, X.J. & Olson, W.K. Web 3DNA: a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. Nucleic Acids Res. 37, W240–W246 (2009).
    Article CAS Google Scholar
  24. Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D. & Zakrzewska, K. CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures. Nucleic Acids Res. 37, 5917–5929 (2009).
    Article CAS Google Scholar
  25. Bingman, C., Jain, S., Zon, S. & Sundaralingam, M. Crystal and molecular structure of the alternating dodecamer d(GCGTACGTACGC) in the A-DNA form: comparison with the isomorphous non-alternating dodecamer d(CCGTACGTACGG). Nucleic Acids Res. 20, 6637–6647 (1992).
    Article CAS Google Scholar
  26. Bingman, C.A., Zon, G. & Sundaralingam, M. Crystal and molecular structure of the A-DNA dodecamer d(CCGTACGTACGG). Choice of fragment helical axis. J. Mol. Biol. 227, 738–756 (1992).
    Article CAS Google Scholar
  27. Drew, H.R. et al. Structure of a B-DNA dodecamer: conformation and dynamics. Proc. Natl. Acad. Sci. USA 78, 2179–2183 (1981).
    Article CAS Google Scholar
  28. Locasale, J.W., Napoli, A.A., Chen, S., Berman, H.M. & Lawson, C.L. Signatures of protein-DNA recognition in free DNA binding sites. J. Mol. Biol. 386, 1054–1065 (2009).
    Article CAS Google Scholar
  29. Leonard, G.A. & Hunter, W.N. Crystal and molecular structure of d(CGTAGATCTACG) at 2.25 A resolution. J. Mol. Biol. 234, 198–208 (1993).
    Article CAS Google Scholar

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