Russian Journal of Genetics

, Volume 52, Issue 11, pp 1117–1123 | Cite as

The miRNA aberrant expression dependence on DNA methylation in HeLa cells treated with mitomycin C

  • V. A. Tarasov
  • N. V. Boyko
  • M. A. Makhotkin
  • E. F. Shin
  • M. G. Tyutyakina
  • I. E. Chikunov
  • A. V. Naboka
  • A. N. Mashkarina
  • A. A. Kirpiy
  • D. G. Matishov
Molecular Genetics


The dependence of expression of miRNAs and their precursors (pre-miRNAs) on the DNA methylation level in HeLa cells 8 days after mitomycin C treatment was studied. A massive parallel DNA sequencing method was applied to analyze miRNA expression. 5-Azacytidine (DNA methylation inhibitor) was added to the medium 6 days after mutagenic agent exposure. The results indicated that the change in expression for some mature miRNAs (39 of 61) was accompanied by the change in the expression of their pre-miRNAs, while there were no significant changes in the expression of pre-miRNA for other mature miRNAs (22 of 61). The aberrant expression was maintained by 8 of 61 mature miRNAs and 6 of 55 pre-miRNAs in the induced HeLa cells after 5-azacytidine treatment. In addition, the expression of more than 90% of miRNAs, which indicated a significant change in expression after mitomycin C treatment, does not depend or depends slightly on the DNA methylation level in HeLa cells without mitomycin C treatment. The results suggest that mitomycin C induces aberrant DNA methylation which affects maintenance of changes in the miRNA expression in cell generations after mutagen treatment.


miRNA DNA methylation mutagen DNA damage response mitomycin C gamma radiation 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Li, M., Marin-Muller, C., Bharadwaj, U., et al., MicroRNAs: control and loss of control in human physiology and disease, World J. Surg., 2009, vol. 33, no. 4, pp. 667–684.CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Friedman, R.C., Farh, K.K.H., Burge, C.B., et al., Most mammalian mRNAs are conserved targets of microRNAs, Genome Res., 2009, vol. 19, no. 1, pp. 92–105.CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Bueno, M.J., De Castro, I., and Malumbres, M., Control of cell proliferation pathways by microRNAs, Cell Cycle, 2008, vol. 7, no. 20, pp. 3143–3148.CrossRefPubMedGoogle Scholar
  4. 4.
    Lima, R.T., Busacca, S., Almeida, G.M., et al., MicroRNA regulation of core apoptosis pathways in cancer, Eur. J. Cancer, 2011, vol. 47, no. 2, pp. 163–174.CrossRefPubMedGoogle Scholar
  5. 5.
    Ivey, K.N. and Srivastava, D., MicroRNAs as regulators of differentiation and cell fate decisions, Cell Stem Cell, 2010, vol. 7, no. 1, pp. 36–41.CrossRefPubMedGoogle Scholar
  6. 6.
    Landau, D.A. and Slack, F.J., MicroRNAs in mutagenesis, genomic instability and DNA repair, Semin. Oncol., 2011, vol. 38, no. 6, pp. 743–751.PubMedGoogle Scholar
  7. 7.
    Hu, H. and Gatti, R.A., MicroRNAs: new players in the DNA damage response, J. Mol. Cell Biol., 2011, vol. 3, no. 3, pp. 151–158.CrossRefPubMedGoogle Scholar
  8. 8.
    Zhang, X. and Lu, X., Posttranscriptional regulation of miRNAs in the DNA damage response, RNA Biol., 2011, vol. 8, no. 6, pp. 960–963.CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Zhang, X., Wan, G., Berger, F.G., et al., The ATM kinase induces microRNA biogenesis in the DNA damage response, Mol. Cell, 2011, vol. 41, no. 4, pp. 371–383.CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Canman, C.E., Lim, D.S., and Cimprich, K.A., Activation of the ATM kinase by ionizing radiation and phosphorylation of p53, Science, 1998, vol. 281, no. 5383, pp. 1677–1679.CrossRefPubMedGoogle Scholar
  11. 11.
    Cortez, D., Guntuku, S., Qin, J., et al., ATR and ATRIP: partners in checkpoint signaling, Science, 2001, vol. 294, no. 5547, pp. 1713–1716.CrossRefPubMedGoogle Scholar
  12. 12.
    Meek, D.W., The p53 response to DNA damage, DNA Repair (Amsterdam), 2004, vol. 3, no. 8–9, pp. 1049–1056.CrossRefGoogle Scholar
  13. 13.
    Ha, M. and Kim, V.N., Regulation of microRNA biogenesis, Nat. Rev. Mol. Cell. Biol., 2014, vol. 15, no. 8, pp. 509–524.CrossRefPubMedGoogle Scholar
  14. 14.
    Metheetrairut, C. and Slack, F.J., MicroRNAs in the ionizing radiation response and in radiotherapy, Curr. Opin. Genet. Dev., 2013, vol. 23, no. 1, pp. 12–19.CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Kraemer, A., Chen, I.P., Henning, S., et al., UVA and UVB irradiation differentially regulate microRNA expression in human primary keratinocytes, PLoS One, 2013, vol. 8, no. 12.Google Scholar
  16. 16.
    Li, Z., Branham, W.S., Dial, S.L., et al., Genomic analysis of microRNA time-course expression in liver of mice treated with genotoxic carcinogen N-ethyl-Nnitrosourea, BMC Genomics, 2010, vol. 11, no. 609.Google Scholar
  17. 17.
    Tarasov, V.A., Matishov, D.G., Shin, E.F., et al., Inheritable changes in miRNAs expression in HeLa cells after X-ray and mitomycin C treatment, Russ. J. Genet., 2014, vol. 50, no. 8, pp. 798–806.CrossRefGoogle Scholar
  18. 18.
    Bhatt, K., Zhou, L., Mi, Q.S., et al., MicroRNA-34a is induced via p53 during cisplatin nephrotoxicity and contributes to cell survival, Mol. Med., 2010, vol. 16, nos. 9–10, pp. 409–416.PubMedPubMedCentralGoogle Scholar
  19. 19.
    Huumonen, K., Korkalainen, M., Viluksela, M., et al., Role of microRNAs and DNA methyltransferases in transmitting induced genomic instability between cell generations, Front. Public Health, 2014, vol. 2, no. 139.Google Scholar
  20. 20.
    Chomczynski, P. and Sacchi, N., Single-step method of RNA isolation by acid guanidinium thiocyanatephenol-chloroform extraction, Anal. Biochem., 1987, vol. 162, pp. 156–159.CrossRefPubMedGoogle Scholar
  21. 21.
    Maniatis, T., Fritsch, E.F., and Sambrook, J., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor: Cold Spring Harbor Lab., 1982.Google Scholar
  22. 22.
    Robinson, M.D., McCarthy, D.J., and Smyth, G.K., edgeR: A bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 2010, vol. 26, pp. 139–140.CrossRefPubMedGoogle Scholar
  23. 23.
    Robinson, M.D. and Smyth, G.K., Small sample estimation of negative binomial dispersion, with applications to SAGE data, Biostatistics, 2008, vol. 9, pp. 321–332.Google Scholar
  24. 24.
    Robinson, M.D. and Oshlack, A., A scaling normalization method for differential expression analysis of RNA-seq data, Genome Biol., 2010, vol. 11, p. R25.CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    McCarthy, D.J., Chen, Y., and Smyth, G.K., Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation, Nucleic Acids Res., 2012, vol. 40, pp. 4288–4297.CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Benjamini, Y. and Hochberg, Y., Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc., Ser. B Methodol., 1995, vol. 57, no. 1, pp. 289–300.Google Scholar
  27. 27.
    Hahn, A.T., Jones, J.T., and Meyer, T., Quantitative analysis of cell cycle phase durations and PC12 differentiation using fluorescent biosensors, Cell Cycle, 2009, vol. 8, no. 7, pp. 1044–1052.CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Volpe, P., Derepression of ornithine-d-transaminase synchronized with the life cycle of Hela cells cultivated in suspension, Biochem. Biophys. Res. Commun., 1969, vol. 34, no. 2, pp. 190–195.CrossRefPubMedGoogle Scholar
  29. 29.
    Halimi, M., Asghari, S.M., Sariri, R., et al., Cellular response to ionizing radiation: a microRNA story, Int. J. Mol. Cell. Med., 2012, vol. 1, no. 4, pp. 178–184.PubMedPubMedCentralGoogle Scholar
  30. 30.
    Liang, G., Li, G., Wang, Y., et al., Aberrant miRNA expression response to UV irradiation in human liver cancer cells, Mol. Med. Rep., 2014, vol. 9, no. 3, pp. 904–910.PubMedGoogle Scholar
  31. 31.
    Li, H., Yu, G., Shi, R., et al., Cisplatin-induced epigenetic activation of miR-34a sensitizes bladder cancer cells to chemotherapy, Mol. Cancer, 2014, vol. 13, no. 8.Google Scholar
  32. 32.
    Wan, G., Mathur, R., Hu, X., et al., MicroRNA response to DNA damage, Trends Biochem. Sci., 2011, vol. 36, no. 9, pp. 478–484.CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Suzuki, H.I. and Miyazono, K., p53 actions on microRNA expression and maturation pathway, Methods Mol. Biol., 2013, vol. 962, pp. 165–181.CrossRefPubMedGoogle Scholar
  34. 34.
    Gregory, R.I., Yan, K.P., Amuthan, G., et al., The microprocessor complex mediates the genesis of microRNAs, Nature, 2004, vol. 432, pp. 235–240.CrossRefPubMedGoogle Scholar
  35. 35.
    Han, J., Lee, Y., Yeom, K.H., et al., The Drosha-DGCR8 complex in primary microRNA processing, Genes Dev., 2004, vol. 18, no. 24, pp. 3016–3027.CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Agranat-Tamir, L., Shomron, N., Sperling, J., et al., Interplay between pre-mRNA splicing and microRNA biogenesis within the supraspliceosome, Nucleic Acids Res., 2014, vol. 42, no. 7, pp. 4640–4651.CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Flores-Jasso, C.F., Arenas-Huertero, C., Reyes, J.L., et al., First step in pre-miRNAs processing by human Dicer, Acta Pharmacol. Sin., 2009, vol. 30, no. 8, pp. 1177–1185.CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Trabucchi, M., Briata, P., Garcia-Mayoral, M., et al., The RNA-binding protein KSRP promotes the biogenesis of a subset of miRNAs, Nature, 2009, vol. 459, no. 7249, pp. 1010–1014.CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Newman, M.A. and Hammond, S.M., Emerging paradigms of regulated microRNA processing, Genes Dev., 2010, vol. 24, no. 11, pp. 1086–1092.CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Antwih, D.A., Gabbara, K.M., Lancaster, W.D., et al., Radiation-induced epigenetic DNA methylation modification of radiation-response pathways, Epigenetics, 2013, vol. 8, no. 8, pp. 839–848.CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Bae, J.H., Kim, J.G., Heo, K., et al., Identification of radiation-induced aberrant hypomethylation in colon cancer, BMC Genomics, 2015, vol. 16, no. 1.Google Scholar
  42. 42.
    Jansson, M.D. and Lund, A.H., MicroRNA and cancer, Mol. Oncol., 2012, vol. 6, no. 6, pp. 590–610.CrossRefPubMedGoogle Scholar
  43. 43.
    Suzuki, H., Maruyama, R., Yamamoto, E., et al., DNA methylation and microRNA dysregulation in cancer, Mol. Oncol., 2012, vol. 6, no. 6, pp. 567–578.CrossRefPubMedGoogle Scholar

Copyright information

© Pleiades Publishing, Inc. 2016

Authors and Affiliations

  • V. A. Tarasov
    • 1
  • N. V. Boyko
    • 1
  • M. A. Makhotkin
    • 1
  • E. F. Shin
    • 1
  • M. G. Tyutyakina
    • 1
  • I. E. Chikunov
    • 1
  • A. V. Naboka
    • 1
  • A. N. Mashkarina
    • 1
  • A. A. Kirpiy
    • 2
  • D. G. Matishov
    • 1
  1. 1.Institute of Arid Zones, Southern Scientific CenterRussian Academy of SciencesRostov-on-DonRussia
  2. 2.InterLabService Co., Ltd.MoscowRussia

Personalised recommendations