Oxidized form of 5-methylcytosine - 5-hydroxymethylcytosine: a new insight into the biological significance in the mammalian genome

Cover Page
Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription or Fee Access


The present review summarizes data on 5-hydroxymethylcytosine - a modification of cytosine with a recently discovered epigenetic effect. The biochemical mechanisms of 5-hydroxymethylcytosine formation and further modification in the mammalian genome are discussed; the role of 5-hydroxymethylcytosine in the epigenetic reprogramming during mammalian gametogenesis and early embryogenesis as well as in the regulation of gene expression is analyzed; data on the diseases and the adverse environmental factors, linked to the DNA hydroxymethyaltion disruptions is shown.

Full Text

Restricted Access

About the authors

Olga Alekseyevna Efimova

D. O. Ott Institute of Obstetrics and Gynecology

Email: efimova_o82@mail.ru
Researcher, PhD. Laboratory for Prenatal Diagnosis of human inherited and inborn disorders

Anna Andreyevna Pendina

D. O. Ott Institute of Obstetrics and Gynecology

Email: pendina@mail.ru
Researcher, PhD. Laboratory for Prenatal Diagnosis of human inherited and inborn disorders

Andrei Vladimirovich Tikhonov

Saint Petersburg State University

Email: tixonov5790@gmail.com
PhD student. Department of Genetics abd Biotechnology

Tatyana Vladimirovna Kuznetzova

D. O. Ott Institute of Obstetrics and Gynecology

PhD, senior researcher. Laboratory for Prenatal Diagnosis of human inherited and inborn disorders

Vladislav Sergeyevich Baranov

D. O. Ott Institute of Obstetrics and Gynecology

Email: baranov@vb2475.spb.edu
Head of the lab., prof. Laboratory for Prenatal Diagnosis of human inherited and inborn disorders


  1. Баранов В. С., Пендина А. А., Кузнецова Т. В. и др. (2005) Некоторые особенности статуса метилирования метафазных хромосом у зародышей человека доимплантационных стадий развития. Цитология. Т. 47, № 8: С. 723-730.
  2. Ефимова О. А., Пендина А. А., Тихонов А. В. и др. (2012) Метилирование ДНК - основной механизм репрограммирования и регуляции генома человека. Медицинская генетика. Т. 11, № 4 (118): С. 10-18.
  3. Пендина А. А., Ефимова О. А., Каминская А. Н. и др. (2005) Иммуноцитохимический анализ статуса метилирования метафазных хромосом человека. Цитология. Т. 47, № 8: C. 731-737.
  4. Al-Mahdawi S., Sandi C., Mouro Pinto R., Pook M. A. (2013) Friedreich ataxia patient tissues exhibit increased 5-hydroxymethylcytosine modification and decreased CTCF binding at the FXN locus. PLoS One. V. 8 (9). e74956.
  5. Beaujean N., Hartshorne G., Cavilla J. et al. (2004) Non-conservation of mammalian preimplantation methylation dynamics. Curr Biol. V. 14: P. R266-R267.
  6. Booth M. J., Branco M. R., Ficz G. et al. (2012) Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science. V. 336: P. 934-937.
  7. Bradley-Whitman M. A., Lovell M. A. (2013) Epigenetic changes in the progression of Alzheimer's disease. Mech Ageing Dev. Available online 3 September 2013. doi: pii: S0047-6374 (13)00096-1.10.1016/ j.mad.2013.08.005.
  8. Carlson B. M. (2009) Human embryology and developmental biology. 4th edition. USA. Mosby. 541 p.
  9. Chia N., Wang L., Lu X., Senut M. C. et al. (2011) Hypothesis: environmental regulation of 5-hydroxymethylcytosine by oxidative stress. Epigenetics. V. 6 (7): P. 853-856.
  10. Chen C. C., Wang K. Y., Shen C. K. (2012) The mammalian de novo DNA methyltransferases DNMT3A and DNMT3B are also DNA 5-hydroxymethylcytosine dehydroxymethylases. J Biol Chem. V. 287: P. 33 116-33 121.
  11. Cliffe L. J., Kieft R., Southern T. et al. (2009) JBP1 and JBP2 are two distinct thymidine hydroxylases involved in J biosynthesis in genomic DNA of African trypanosomes. Nucleic Acids Res. V. 37: P. 1452-1462.
  12. Cortázar D., Kunz C., Selfridge J. et al. (2011) Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability. Nature. V. 470 (7334): P. 419-423.
  13. Cortellino S., Xu J., Sannai M. et al. (2011) Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell. V. 146 (1): P. 67-79.
  14. Ficz G., Branco M. R., Seisenberger S. et al. (2011) Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature. V. 473: P. 398-402.
  15. Fulka H., Mrazek M., Tepla O., Fulka Jr. J. (2004) DNA methylation pattern in human zygotes and developing embryos. Reproduction. V. 128: P. 703-708.
  16. Gambichler T., Sand M., Skrygan M. (2013) Loss of 5-hydroxymethylcytosine and ten-eleven translocation 2 protein expression in malignant melanoma. Melanoma Res. V. 23 (3): P. 218-220.
  17. Gu T. P., Guo F., Yang H. et al. (2011) The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature. V. 477 (7366): P. 606-610.
  18. Guo J. U., Su Y., Zhong C. et al. (2011) Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell. V. 145: P. 423-434.
  19. Hattman S., Fukasawa T. (1963) Host-induced modification of T-even phages due to defective glucosylation of their DNA. Proc. Natl. Acad. Sci. USA. V. 50: P. 297-300.
  20. He Y. F., Li B. Z., Li Z. et al. (2011) Tet-mediated formation of 5-Carboxylcytosine and its excision by TDG in mammalian DNA. Science. V. 333: P. 1303-1307.
  21. Iqbal K., Jin S. G., Pfeifer G. P., Szabó P. E. (2011) Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc. Natl. Acad. Sci. USA. V. 108 (9): P. 3642-3647.
  22. Inoue A., Shen L., Dai Q., He C., Zhang Y. (2011) Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development. Cell Res. V. 21 (12): P. 1670-1676.
  23. Inoue A., Zhang Y. (2011) Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science. V. 334 (6053): P. 194.
  24. Ito S., D’Alessio A. C., Taranova O. V. et al. (2010) Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature. V. 466: P. 1129-1133.
  25. Ito S., Shen L., Dai Q. et al. (2011) Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science. V. 333 (6047): P. 1229-1230.
  26. Jäwert F., Hasséus B., Kjeller G. et al. (2013) Loss of 5-Hydroxymethylcytosine and TET2 in Oral Squamous Cell Carcinoma. Anticancer Res. V. 33 (10): P. 4325-4328.
  27. Jefferson W. N., Chevalier D. M., Phelps J. Y. et al. (2013) Persistently altered epigenetic marks in the mouse uterus after neonatal estrogen exposure. Mol. Endocrinol. V. 27 (10): P. 1666-1677.
  28. Kagiwada S., Kurimoto K., Hirota T. et al. (2012) Replication-coupled passive DNA demethylation for the erasure of genome imprints in mice. EMBO J. V. 32: P. 340-353.
  29. Kornberg A., Zimmerman S. B., Kornberg S. R., Josse J. (1959) Enzymatic synthesis of deoxyribonucleic acid. Influence of bacteriophage T2 on the synthetic pathway in host cells. Proc. Natl. Acad. Sci. USA. V. 45: P. 772-785.
  30. Kothari R. M., Shankar V. (1976) 5-Methylcytosine content in the vertebrate deoxyribonucleic acids: species specificity. J Mol Evol. V. 7: P. 325-329.
  31. Kriaucionis S., Heintz N. (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science. V. 324: P. 929-930.
  32. Li W., Liu M. (2011) Distribution of 5-hydroxymethylcytosine in different human tissues. J Nucleic Acids. V. 2011. Article ID 870726. 5 pages.
  33. Lian C. G., Xu Y., Ceol C. et al. (2012) Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell. V. 150 (6): P. 1135-1146.
  34. Liu C., Liu L., Chen X. et al. (2013) Decrease of 5-hydroxymethylcytosine is associated with progression of hepatocellular carcinoma through downregulation of TET1. PLoS One. V. 8 (5). e62828.
  35. Maiti A., Drohat A. C. (2011) Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites. J Biol Chem. V. 286 (41): P. 35 334-35 338.
  36. Nakamura T., Arai Y., Umehara H. et al. (2007) PGC7/Stella protects against DNA demethylation in early embryogenesis. Nature Cell Biol. V. 9 (1): P. 64-71.
  37. Nakamura T., Liu Y. J., Nakashima H. et al. (2012) PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos. Nature. V. 486 (7403): P. 415-419.
  38. Nestor C. E., Ottaviano R., Reddington J. et al. (2012) Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes. Genome Res. V. 22 (3): P. 467-477.
  39. Pastor W. A., Pape U. J., Huang Y. et al. (2011) Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature. V. 473: P. 394-397.
  40. Pendina A. A., Efimova O. A., Fedorova I.D et al. (2011) DNA methylation patterns of metaphase chromosomes in human preimplantation embryos. Cytogenetic and Genome Research. V. 132 (1-2): P. 1-7.
  41. Penn N. W., Suwalski R., O'Riley C. et al. (1972) The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid. Biochem J. V. 126: P. 781-790.
  42. Pfaffeneder T., Hackner B., Truss M. et al. (2011) The discovery of 5-formylcytosine in embryonic stem cell DNA. Angew. Chem. Int. Ed. Engl. V. 50 (31): P. 7008-7012.
  43. Salvaing J., Aguirre-Lavin T., Boulesteix C. et al. (2012) 5-Methylcytosine and 5-hydroxymethylcytosine spatiotemporal profiles in the mouse zygote. PLoS One. V. 7 (5). e38156.
  44. Shedlovsky A., Brenner S. (1963) A chemical basis for the host-induced modification of T-even bacteriophages. Proc. Natl. Acad. Sci. USA. V. 50: P. 300-305.
  45. Shen L., Zhang Y. (2013) 5-Hydroxymethylcytosine: generation, fate, and genomic distribution. Curr. Opin. Cell Biol. V. 25 (3); P. 289-296.
  46. Someya S., Yu W., Hallows W. C. et al. (2010) Sirt3 mediates reduction of oxidative damage and prevention of age-related hearing loss under caloric restriction. Cell. V. 143 (5): P. 802-812.
  47. Song C. X., Szulwach K. E., Fu Y. et al. (2011) Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat. Biotechnol. V. 29: P. 68-72.
  48. Song C. X., He C. (2012) Balance of DNA methylation and demethylation in cancer development. Genome Biol. V. 13: P. 173.
  49. Steinberg J. J., Cajigas A., Brownlee M. (1992) Enzymatic shot-gun 50-phosphorylation and 30-sister phosphate exchange: a two-dimensional thin-layer chromatographic technique to measure DNA deoxynucleotide modification. J Chromatogr. V. 574: P. 41-55.
  50. Stroud H., Feng S., Morey Kinney S. et al. (2011) 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol. V. 12: P. R54.
  51. Szulwach K. E., Li X., Li Y. et al. (2011a) 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopmentand aging. Nat. Neurosci. V. 14: P. 1607-1616.
  52. Szulwach K. E., Li X., Li Y. et al. (2011b) Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet. V. 7 (6). e1002154.
  53. Tahiliani M., Koh K. P., Shen Y. et al. (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. V. 324: P. 930-935.
  54. Thomson J. P., Lempiainen H., Hackett J. A. et al. (2012) Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome. Genome Biol. V. 13: P. R93.
  55. Valinluck V., Sowers L. C. (2007) Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1. Cancer Res. V. 67: P. 946-950.
  56. Wang T., Pan Q., Lin L. et al. (2012) Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum. Hum. Mol. Genet. V. 21: P. 5500-5510.
  57. Wang F., Yang Y., Lin X., Wang J. Q. et al. (2013) Genome-wide loss of 5-hmC is a novel epigenetic feature of Huntington's disease. Hum. Mol. Genet. V. 22 (18): P. 3641-3653.
  58. Williams K., Christensen J., Pedersen M. T. et al. (2011) TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature. V. 473: P. 343-348.
  59. Wossidlo M., Arand J., Sebastiano V. et al. (2010) Dynamic link of DNA demethylation, DNA strand breaks and repair in mouse zygotes. EMBO J. V. 29 (11): P. 1877-1888.
  60. Wossidlo M., Nakamura T., Lepikhov K. et al. (2011) 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nat. Commun. V. 2; P. 241.
  61. Wu H., D’Alessio A. C., Ito S. et al. (2011) Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev. V. 25: P. 679-684.
  62. Wyatt G. R., Cohen S. S. (1952) A new pyrimidine base from bacteriophage nucleic acids. Nature. V. 170: P. 1072-1073.
  63. Xu Y., Zhang J. J., Grifo J. A., Krey L. C. (2005) DNA methylation patterns in human tripronucleate zygotes. Molecular Human Reproduction. V. 11 (3): P. 167-171.
  64. Xu Y., Wu F., Tan L. et al. (2011) Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol. Cell. V. 42: P. 451-464.
  65. Yamaguchi S., Hong K., Liu R. et al. (2012) Tet1 controls meiosis by regulating meiotic gene expression. Nature. V. 492: P. 443-447.
  66. Yamaguchi S., Hong K., Liu R. et al. (2013) Dynamics of 5-methylcytosine and 5-hydroxymethylcytosine during germ cell reprogramming. Cell Res. V. 23 (3): P. 329-339.
  67. Yang H., Liu Y., Bai F. et al. (2013) Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation. Oncogene. V. 32 (5): P. 663-669.
  68. Yu Z., Genest P. A., ter Riet B. et al. (2007) The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase. Nucleic Acids Res. V. 35: P. 2107-2115.
  69. Yu M., Hon G. C., Szulwach K. E. et al. (2012) Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell. V. 149: P. 1368-1380.
  70. Zhu B., Zheng Y., Angliker H. et al. (2000) 5-Methylcytosine DNA glycosylase activity is also present in the human MBD4 (G/T mismatch glycosylase) and in a related avian sequence. Nucleic Acids Res. V. 28 (21): P. 4157-4165.



Abstract - 750

PDF (Russian) - 268


Article Metrics

Metrics Loading ...



Copyright (c) 2014 Efimova O.A., Pendina A.A., Tikhonov A.V., Kuznetzova T.V., Baranov V.S.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies