10038 Nucleic Acids Research, 2015, Vol. 43, No. 20
2. Morison,I.M., Ramsay,J.P. and Spencer,H.G. (2005) A census of
mammalian imprinting. Trends Genet., 21, 457–465.
3. Miranda,T.B. and Jones,P.A. (2007) DNA methylation: the nuts and
bolts of repression. J. Cell. Physiol., 213, 384–390.
26. Xu,S., Li,W., Zhu,J., Wang,R., Li,Z., Xu,G.L. and Ding,J. (2013)
Crystal structures of isoorotate decarboxylases reveal a novel
catalytic mechanism of 5-carboxyl-uracil decarboxylation and shed
light on the search for DNA decarboxylase. Cell Res., 23, 1296–1309.
27. Neidigh,J.W., Darwanto,A., Williams,A.A., Wall,N.R. and
Sowers,L.C. (2009) Cloning and characterization of Rhodotorula
glutinis thymine hydroxylase. Chem. Res. Toxicol., 22, 885–893.
28. Thornburg,L.D., Lai,M.T., Wishnok,J.S. and Stubbe,J. (1993) A
non-heme iron protein with heme tendencies: an investigation of the
substrate specificity of thymine hydroxylase. Biochemistry, 32,
14023–14033.
29. Holme,E. (1975) A kinetic study of thymine 7-hydroxylase from
Neurospora crassa. Biochemistry, 14, 4999–5003.
30. Otwinowski,Z. and Minor,W. (1997) Processing of X-ray diffraction
data collected in oscillation mode. Methods Enzymol., 276, 307–326.
31. Adams,P.D., Afonine,P.V., Bunkoczi,G., Chen,V.B., Davis,I.W.,
Echols,N., Headd,J.J., Hung,L.W., Kapral,G.J.,
4. Suzuki,M.M. and Bird,A. (2008) DNA methylation landscapes:
provocative insights from epigenomics. Nat. Rev. Genet., 9, 465–476.
5. Tahiliani,M., Koh,K.P., Shen,Y., Pastor,W.A., Bandukwala,H.,
Brudno,Y., Agarwal,S., Iyer,L.M., Liu,D.R., Aravind,L. et al. (2009)
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in
mammalian DNA by MLL partner TET1. Science, 324, 930–935.
6. Iyer,L.M., Tahiliani,M., Rao,A. and Aravind,L. (2009) Prediction of
novel families of enzymes involved in oxidative and other complex
modifications of bases in nucleic acids. Cell Cycle, 8, 1698–1710.
7. Pfaffeneder,T., Hackner,B., Truss,M., Munzel,M., Muller,M.,
Deiml,C.A., Hagemeier,C. and Carell,T. (2011) The discovery of
5-formylcytosine in embryonic stem cell DNA. Angew. Chem.-Int.
Edit., 50, 7008–7012.
8. Ito,S., Shen,L., Dai,Q., Wu,S.C., Collins,L.B., Swenberg,J.A., He,C.
and Zhang,Y. (2011) Tet proteins can convert 5-methylcytosine to
5-formylcytosine and 5-carboxylcytosine. Science, 333, 1300–1303.
9. He,Y.F., Li,B.Z., Li,Z., Liu,P., Wang,Y., Tang,Q., Ding,J., Jia,Y.,
Chen,Z., Li,L. et al. (2011) Tet-mediated formation of
5-carboxylcytosine and its excision by TDG in mammalian DNA.
Science, 333, 1303–1307.
10. Zhang,L., Lu,X., Lu,J., Liang,H., Dai,Q., Xu,G.L., Luo,C., Jiang,H.
and He,C. (2012) Thymine DNA glycosylase specifically recognizes
5-carboxylcytosine-modified DNA. Nat. Chem. Biol., 8, 328–330.
11. Wu,H. and Zhang,Y. (2014) Reversing DNA methylation:
mechanisms, genomics, and biological functions. Cell, 156, 45–68.
12. Pastor,W.A., Aravind,L. and Rao,A. (2013) TETonic shift: biological
roles of TET proteins in DNA demethylation and transcription. Nat.
Rev. Mol. Cell Biol., 14, 341–356.
13. Cimmino,L., Abdel-Wahab,O., Levine,R.L. and Aifantis,I. (2011)
TET family proteins and their role in stem cell differentiation and
transformation. Cell Stem cell, 9, 193–204.
14. Branco,M.R., Ficz,G. and Reik,W. (2012) Uncovering the role of
5-hydroxymethylcytosine in the epigenome. Nat. Rev. Genet., 13,
7–13.
15. Huang,Y. and Rao,A. (2014) Connections between TET proteins and
aberrant DNA modification in cancer. Trends Genet., 30, 464–474.
16. Hashimoto,H., Pais,J.E., Zhang,X., Saleh,L., Fu,Z.Q., Dai,N.,
Correa,I.R. Jr, Zheng,Y. and Cheng,X. (2014) Structure of a
Naegleria Tet-like dioxygenase in complex with 5-methylcytosine
DNA. Nature, 506, 391–395.
17. Hu,L., Li,Z., Cheng,J., Rao,Q., Gong,W., Liu,M., Shi,Y.G., Zhu,J.,
Wang,P. and Xu,Y. (2013) Crystal structure of TET2-DNA complex:
insight into TET-mediated 5mC oxidation. Cell, 155, 1545–1555.
18. Fink,R.M. and Fink,K. (1962) Utilization of radiocarbon from
thymidine and other precursors of ribonucleic acid in Neurospora
crassa. J. Biol. Chem., 237, 2289–2290.
Grosse-Kunstleve,R.W. et al. (2010) PHENIX: a comprehensive
Python-based system for macromolecular structure solution. Acta
Crystallogr., D66, 213–221.
32. Emsley,P. and Cowtan,K. (2004) COOT: model-building tools for
molecular graphics. Acta Crystallogr., D60, 2126–2132.
33. Murshudov,G.N., Vagin,A.A. and Dodson,E.J. (1997) Refinement of
macromolecular structures by the maximum-likelihood method. Acta
Crystallogr., D53, 240–255.
34. Winn,M.D., Ballard,C.C., Cowtan,K.D., Dodson,E.J., Emsley,P.,
Evans,P.R., Keegan,R.M., Krissinel,E.B., Leslie,A.G., McCoy,A.
et al. (2011) Overview of the CCP4 suite and current developments.
Acta Crystallogr., D67, 235–242.
35. Laskowski,R.A., Macarthur,M.W., Moss,D.S. and Thornton,J.M.
(1993) PROCHECK: a program to check the stereochemical quality
of protein structures. J. Appl. Crystallogr., 26, 283–291.
36. Luo,L., Pappalardi,M.B., Tummino,P.J., Copeland,R.A.,
Fraser,M.E., Grzyska,P.K. and Hausinger,R.P. (2006) An assay for
Fe(II)/2-oxoglutarate-dependent dioxygenases by enzyme-coupled
detection of succinate formation. Anal. Biochem., 353, 69–74.
37. Aik,W., McDonough,M.A., Thalhammer,A., Chowdhury,R. and
Schofield,C.J. (2012) Role of the jelly-roll fold in substrate binding by
2-oxoglutarate oxygenases. Curr. Opin. Struct. Biol., 22, 691–700.
38. Ergel,B., Gill,M.L., Brown,L., Yu,B., Palmer,A.G. 3rd and Hunt,J.F.
(2014) Protein dynamics control the progression and efficiency of the
catalytic reaction cycle of the Escherichia coli DNA-repair enzyme
AlkB. J. Biol. Chem., 289, 29584–29601.
39. Yu,B., Edstrom,W.C., Benach,J., Hamuro,Y., Weber,P.C.,
Gibney,B.R. and Hunt,J.F. (2006) Crystal structures of catalytic
complexes of the oxidative DNA/RNA repair enzyme AlkB. Nature,
439, 879–884.
40. McDonough,M.A., Loenarz,C., Chowdhury,R., Clifton,I.J. and
Schofield,C.J. (2010) Structural studies on human 2-oxoglutarate
dependent oxygenases. Curr. Opin. Struct. Biol., 20, 659–672.
41. Harding,M.M. (2001) Geometry of metal-ligand interactions in
proteins. Acta Crystallogr., D57, 401–411.
42. Valegard,K., van Scheltinga,A.C., Lloyd,M.D., Hara,T.,
Ramaswamy,S., Perrakis,A., Thompson,A., Lee,H.J., Baldwin,J.E.,
Schofield,C.J. et al. (1998) Structure of a cephalosporin synthase.
Nature, 394, 805–809.
19. Shaffer,P.M., McCroskey,R.P. and Abbott,M.T. (1972) Substrate
specificity of the hydroxylase reaction in which thymidine is converted
to thymine ribonucleoside. Biochim. Biophys. Acta, 258, 387–394.
20. Liu,C.K., Hsu,C.A. and Abbott,M.T. (1973) Catalysis of three
sequential dioxygenase reactions by thymine 7-hydroxylase. Arch.
Biochem. Biophys., 159, 180–187.
21. Holme,E., Lindstedt,G., Lindstedt,S. and Tofft,M. (1971) 18-O
studies of the 2-ketoglutarate-dependent sequential oxygenation of
thymine to 5-carboxyuracil. J. Biol. Chem., 246, 3314–3319.
22. Watanabe,M.S., McCroskey,R.P. and Abbott,M.T. (1970) The
enzymatic conversion of 5-formyluracil to uracil 5-carboxylic acid. J.
Biol. Chem., 245, 2023–2026.
23. Abbott,M.T., Schandl,E.K., Lee,R.F., Parker,T.S. and Midgett,R.J.
(1967) Cofactor requirements of thymine 7-hydroxylase. Biochim.
Biophys. Acta, 132, 525–528.
43. Clifton,I.J., McDonough,M.A., Ehrismann,D., Kershaw,N.J.,
Granatino,N. and Schofield,C.J. (2006) Structural studies on
2-oxoglutarate oxygenases and related double-stranded beta-helix
fold proteins. J. Inorg. Biochem., 100, 644–669.
44. Hausinger,R.P. (2004) FeII/alpha-ketoglutarate-dependent
hydroxylases and related enzymes. Crit. Rev. Biochem. Mol. Biol., 39,
21–68.
45. Holm,L. and Rosenstrom,P. (2010) Dali server: conservation
mapping in 3D. Nucleic Acids Res., 38, W545–W549.
24. Palmatier,R.D., McCroskey,R.P. and Abbott,M.T. (1970) The
enzymatic conversion of uracil 5-carboxylic acid to uracil and carbon
dioxide. J. Biol. Chem., 245, 6706–6710.
25. Smiley,J.A., Angelot,J.M., Cannon,R.C., Marshall,E.M. and
Asch,D.K. (1999) Radioactivity-based and spectrophotometric assays
for isoorotate decarboxylase: identification of the thymidine salvage
pathway in lower eukaryotes. Anal. Biochem., 266, 85–92.
46. Wu,H. and Zhang,Y. (2011) Mechanisms and functions of Tet
protein-mediated 5-methylcytosine oxidation. Genes Dev., 25,
2436–2452.
47. Shen,L., Wu,H., Diep,D., Yamaguchi,S., D’Alessio,A.C., Fung,H.L.,
Zhang,K. and Zhang,Y. (2013) Genome-wide analysis reveals TET-
and TDG-dependent 5-methylcytosine oxidation dynamics. Cell, 153,
692–706.