Abstract
In mammals, DNA methyltransferases create 5-methylcytosines (5mC) predominantly at CpG dinucleotides. 5mC oxidases convert 5mC in three consecutive oxidation steps to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and then 5-carboxylcytosine (5caC). Upon irradiation with UV light, dipyrimidines containing C, 5mC and 5hmC are known to form cyclobutane pyrimidine dimers (CPDs) as major DNA photolesions. However, the photobiology of 5fC and 5caC has remained largely unexplored. Here, we tested a series of oligonucleotides with single or multiple positions carrying cytosine (C), 5mC, 5hmC, 5fC, or 5caC and irradiated them with different sources of UV irradiation. Although UVC radiation produced CPDs near dipyrimidines containing all types of modified cytosine bases, UVB radiation produced by far the highest levels of CPDs near 5caC-containing sequences. Dipyrimidines one or two nucleotide positions adjacent to 5caC but not always those involving this modified base directly were the major sites for these prominent UVB photoproducts. This selectivity did not depend on whether 5caC was present on one or both DNA strands at CpG sequences. We also observed a tendency of the 5caC-containing DNA strands to undergo apparent covalent crosslinking. This reaction occurred with UVB or UVC, but not with UVA irradiation. Our data show that 5-carboxylcytosine, although generally a rare base in the genome, can nonetheless make a strong contribution to sequence-specific DNA damage perhaps by acting as a DNA-intrinsic photosensitizer.
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References
Aparici-Espert, I., Garcia-Lainez, G., Andreu, I., Miranda, M. A., & Lhiaubet-Vallet, V. (2018). Oxidatively generated lesions as internal photosensitizers for pyrimidine dimerization in DNA. ACS Chemical Biology, 13(3), 542–547. https://doi.org/10.1021/acschembio.7b01097.
Banyasz, A., et al. (2012). Electronic excited states responsible for dimer formation upon UV absorption directly by thymine strands: joint experimental and theoretical study. Journal of the American Chemical Society, 134(36), 14834–14845. https://doi.org/10.1021/ja304069f.
Banyasz, A., et al. (2016). Effect of C5-methylation of cytosine on the UV-induced reactivity of duplex DNA: conformational and electronic factors. The Journal of Physical Chemistry B, 120(18), 4232–4242. https://doi.org/10.1021/acs.jpcb.6b03340.
Besaratinia, A., et al. (2005). DNA lesions induced by UV A1 and B radiation in human cells: comparative analyses in the overall genome and in the p53 tumor suppressor gene. Proceedings of the National Academy of Sciences of the United States of America, 102(29), 10058–10063.
Beukers, R., & Berends, W. (1960). Isolation and identification of the irradiation product of thymine. Biochimica et Biophysica Acta, 41, 550–551. https://doi.org/10.1016/0006-3002(60)90063-9.
Cadet, J., & Douki, T. (2011). Oxidatively generated damage to DNA by UVA radiation in cells and human skin. Journal of Investigative Dermatology, 131(5), 1005–1007. https://doi.org/10.1038/jid.2011.51.
Cadet, J., Douki, T., & Ravanat, J. L. (2015). Oxidatively generated damage to cellular DNA by UVB and UVA radiation. Photochemistry and Photobiology, 91(1), 140–155. https://doi.org/10.1111/php.12368.
Cadet, J., Mouret, S., Ravanat, J. L., & Douki, T. (2012). Photoinduced damage to cellular DNA: direct and photosensitized reactions. Photochemistry and Photobiology, 88(5), 1048–1065. https://doi.org/10.1111/j.1751-1097.2012.01200.x.
Cannistraro, V. J., Pondugula, S., Song, Q., & Taylor, J. S. (2015). Rapid deamination of cyclobutane pyrimidine dimer photoproducts at TCG sites in a translationally and rotationally positioned nucleosome in vivo. Journal of Biological Chemistry, 290(44), 26597–26609. https://doi.org/10.1074/jbc.M115.673301.
Colquitt, B. M., Allen, W. E., Barnea, G., & Lomvardas, S. (2013). Alteration of genic 5-hydroxymethylcytosine patterning in olfactory neurons correlates with changes in gene expression and cell identity. Proceedings of the National Academy of Sciences of the United States of America, 110(36), 14682–14687. https://doi.org/10.1073/pnas.1302759110.
Dai, Q., Sanstead, P. J., Peng, C. S., Han, D., He, C., & Tokmakoff, A. (2016). Weakened N3 hydrogen bonding by 5-formylcytosine and 5-carboxylcytosine reduces their base-pairing stability. ACS Chemical Biology, 11(2), 470–477. https://doi.org/10.1021/acschembio.5b00762.
Dodson, M. L., & Lloyd, R. S. (1989). Structure–function studies of the T4 endonuclease V repair enzyme. Mutation Research, 218(2), 49–65. https://doi.org/10.1016/0921-8777(89)90011-6.
Douki, T., Reynaud-Angelin, A., Cadet, J., & Sage, E. (2003). Bipyrimidine photoproducts rather than oxidative lesions are the main type of DNA damage involved in the genotoxic effect of solar UVA radiation. Biochemistry, 42(30), 9221–9226. https://doi.org/10.1021/bi034593c.
Drouin, R., & Therrien, J. P. (1997). UVB-induced cyclobutane pyrimidine dimer frequency correlates with skin cancer mutational hotspots in p53. Photochemistry and Photobiology, 66(5), 719–726. https://doi.org/10.1111/j.1751-1097.1997.tb03213.x.
Globisch, D., et al. (2010). Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS ONE, 5(12), e15367. https://doi.org/10.1371/journal.pone.0015367.
Hahn, M. A., et al. (2019). Reprogramming of DNA methylation at NEUROD2-bound sequences during cortical neuron differentiation. Sciences Advances, 23, eaax0080.
He, Y. F., et al. (2011). Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science, 333(6047), 1303–1307. https://doi.org/10.1126/science.1210944.
Huix-Rotllant, M., Brazard, J., Improta, R., Burghardt, I., & Markovitsi, D. (2015). Stabilization of mixed Frenkel-charge transfer excitons extended across both strands of guanine-cytosine DNA duplexes. The Journal of Physical Chemistry Letters, 6(12), 2247–2251. https://doi.org/10.1021/acs.jpclett.5b00813.
Ito, S., et al. (2011). Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science, 333(6047), 1300–1303. https://doi.org/10.1126/science.1210597.
Johns, H. E., Rapaport, S. A., & Delbrueck, M. (1962). Photochemistry of thymine dimers. Journal of Molecular Biology, 4, 104–114. https://doi.org/10.1016/s0022-2836(62)80042-4.
Kim, S. I., Jin, S. G., & Pfeifer, G. P. (2013). Formation of cyclobutane pyrimidine dimers at dipyrimidines containing 5-hydroxymethylcytosine. Photochemical and Photobiological Sciences, 12(8), 1409–1415. https://doi.org/10.1039/c3pp50037c.
Lee, D. H., & Pfeifer, G. P. (2003). Deamination of 5-methylcytosines within cyclobutane pyrimidine dimers is an important component of UVB mutagenesis. Journal of Biological Chemistry (in press).
Markovitsi, D. (2016). UV-induced DNA damage: the role of electronic excited states. Photochemistry and Photobiology, 92(1), 45–51. https://doi.org/10.1111/php.12533.
Martinez-Fernandez, L., Banyasz, A., Esposito, L., Markovitsi, D., & Improta, R. (2017). UV-induced damage to DNA: effect of cytosine methylation on pyrimidine dimerization. Signal Transduction and Targeted Therapy, 2, 17021. https://doi.org/10.1038/sigtrans.2017.21.
Mitchell, D. L., & Fernandez, A. A. (2011). Different types of DNA damage play different roles in the etiology of sunlight-induced melanoma. Pigment Cell & Melanoma Research, 24(1), 119–124. https://doi.org/10.1111/j.1755-148X.2010.00789.x.
Ngo, T. T., et al. (2016). Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability. Nature Communications, 7, 10813. https://doi.org/10.1038/ncomms10813.
Pfeifer, G. P. (2020). Mechanisms of UV-induced mutations and skin cancer. Genome Instability & Disease, 1, 99–113.
Premi, S., & Brash, D. E. (2016). Chemical excitation of electrons: a dark path to melanoma. DNA Repair, 44, 169–177. https://doi.org/10.1016/j.dnarep.2016.05.023.
Rochette, P. J., et al. (2003). UVA-induced cyclobutane pyrimidine dimers form predominantly at thymine–thymine dipyrimidines and correlate with the mutation spectrum in rodent cells. Nucleic Acids Research, 31(11), 2786–2794.
Rochette, P. J., Lacoste, S., Therrien, J. P., Bastien, N., Brash, D. E., & Drouin, R. (2009). Influence of cytosine methylation on ultraviolet-induced cyclobutane pyrimidine dimer formation in genomic DNA. Mutation Research, 665(1–2), 7–13. https://doi.org/10.1016/j.mrfmmm.2009.02.008.
Sage, E., Lamolet, B., Brulay, E., Moustacchi, E., Chteauneuf, A., & Drobetsky, E. A. (1996). Mutagenic specificity of solar UV light in nucleotide excision repair-deficient rodent cells. Proceedings of the National academy of Sciences of the United States of America, 93, 176–180.
Schreier, W. J., Gilch, P., & Zinth, W. (2015). Early events of DNA photodamage. Annual Review of Physical Chemistry, 66, 497–519. https://doi.org/10.1146/annurev-physchem-040214-121821.
Setlow, R. B., & Setlow, J. K. (1962). Evidence that ultraviolet-induced thymine dimers in DNA cause biological damage. Proceedings of the National Academy of Sciences of the United States of America, 48, 1250–1257. https://doi.org/10.1073/pnas.48.7.1250.
Sharonov, A., Gustavsson, T., Marguet, S., & Markovitsi, D. (2003). Photophysical properties of 5-methylcytidine. Photochemical and Photobiological Sciences, 2(4), 362–364.
Shen, L., et al. (2013). Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics. Cell, 153(3), 692–706. https://doi.org/10.1016/j.cell.2013.04.002.
Tahiliani, M., et al. (2009). Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science, 324(5929), 930–935.
Takaya, T., Su, C., de La Harpe, K., Crespo-Hernandez, C. E., & Kohler, B. (2008). UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases. Proceedings of the National Academy of Sciences of the United States of America, 105(30), 10285–10290. https://doi.org/10.1073/pnas.0802079105.
Tommasi, S., Denissenko, M. F., & Pfeifer, G. P. (1997). Sunlight induces pyrimidine dimers preferentially at 5-methylcytosine bases. Cancer Research, 57, 4727–4730.
Tornaletti, S., & Pfeifer, G. P. (1995). Complete and tissue-independent methylation of CpG sites in the p53 gene: implications for mutations in human cancers. Oncogene, 10, 1493–1499.
Vendrell-Criado, V., Rodriguez-Muniz, G. M., Lhiaubet-Vallet, V., Cuquerella, M. C., & Miranda, M. A. (2016). The (6–4) dimeric lesion as a DNA photosensitizer. ChemPhysChem, 17(13), 1979–1982. https://doi.org/10.1002/cphc.201600154.
Vu, B., Cannistraro, V. J., Sun, L., & Taylor, J. S. (2006). DNA synthesis past a 5-methylC-containing cis-syn-cyclobutane pyrimidine dimer by yeast pol eta is highly nonmutagenic. Biochemistry, 45(30), 9327–9335.
Wacker, A., Dellweg, H., & Jacherts, D. (1962). Thymine dimerization and survival of bacteria. Journal of Molecular Biology, 4, 410–412. https://doi.org/10.1016/s0022-2836(62)80022-9.
Wang, X., et al. (2019). Ultrafast Intersystem Crossing in Epigenetic DNA Nucleoside 2’-Deoxy-5-formylcytidine. The Journal of Physical Chemistry B, 123(27), 5782–5790. https://doi.org/10.1021/acs.jpcb.9b04361.
Yasuda, S., & Sekiguchi, M. (1970). T4 endonuclease involved in repair of DNA. Proceedings of the National Academy of Sciences of the United States of America, 67(4), 1839–1845. https://doi.org/10.1073/pnas.67.4.1839.
Yoon, J.-H., Lee, C.-S., O’Connor, T., Yasui, A., & Pfeifer, G. P. (2000). The DNA damage spectrum produced by simulated sunlight. Journal of Molecular Biology, 299, 681–693.
You, Y. H., Lee, D. H., Yoon, J. H., Nakajima, S., Yasui, A., & Pfeifer, G. P. (2001). Cyclobutane pyrimidine dimers are responsible for the vast majority of mutations induced by UVB irradiation in mammalian cells. Journal of Biological Chemistry, 276, 44688–44694.
You, Y.-H., Li, C., & Pfeifer, G. P. (1999). Involvement of 5-methylcytosine in sunlight-induced mutagenesis. Journal of Molecular Biology, 293, 493–503.
You, Y. H., & Pfeifer, G. P. (2001). Similarities in sunlight-induced mutational spectra of CpG-methylated transgenes and the p53 gene in skin cancer point to an important role of 5-methylcytosine residues in solar UV mutagenesis. Journal of Molecular Biology, 305, 389–399.
You, Y. H., Szabo, P. E., & Pfeifer, G. P. (2000). Cyclobutane pyrimidine dimers form preferentially at the major p53 mutational hotspot in UVB-induced mouse skin tumors. Carcinogenesis, 21(11), 2113–2117. https://doi.org/10.1093/carcin/21.11.2113.
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This study was supported by NIH grant R37 ES006070 to G.P.P.
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GPP designed the research. SIK performed the research. SIK and GPP analyzed the data. GPP wrote the manuscript.
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Kim, SI., Pfeifer, G.P. The epigenetic DNA modification 5-carboxylcytosine promotes high levels of cyclobutane pyrimidine dimer formation upon UVB irradiation. GENOME INSTAB. DIS. 2, 59–69 (2021). https://doi.org/10.1007/s42764-020-00030-x
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DOI: https://doi.org/10.1007/s42764-020-00030-x