Skip to main content
SpringerLink
Log in

Identification and validation of novel microrna molecule from the Pelodiscus sinensis by bioinformatics approaches

  • Published:
Russian Journal of Bioorganic Chemistry Aims and scope Submit manuscript

Abstract

MicroRNAs (miRNAs) are a group of endogenous, short non-coding RNAs with the length of about 22 nt, which mediate gene expression at the post-transcriptional level through mRNA degradation or translational repression. Among them, some are highly evolutionally conserved in the animal kingdom; this provides a powerful strategy for identifying miRNAs in new species. The Chinese soft-shelled turtle (Pelodiscus sinensis) is one of the most important freshwater aquaculture reptilian species in China, but related miRNAs have not been identified up to now. In the present study, a total of 10 Pelodiscus sinensis miRNAs were identified according to Pelodiscus sinensis ESTs and GSSs information in NCBI database by bioinformatics approaches. The RT-PCR-based assays were performed and found that 10 Pelodiscus sinensis miRNAs were expressed. Using these miRNAs, 22 target genes were identified. These genes encode 22 proteins involved in metabolism, signal transduction, transcriptional regulation, and development. These miRNAs and their targets will serve as useful resources for their functional analyses in miRNA-regulated processes in Pelodiscus sinensis breeding and genetic research.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Zhou, X., Guo, Q., and Dai, H., Dev. Comp. Immunol., 2009, vol. 33, pp. 838–847.

    Article  CAS  PubMed  Google Scholar 

  2. Zhang, W., Rui, L., Zhang, J., Yu, X., Yuan, F., Yan, L., Zhang, Z., Wan, Z., Shao, Q., Qi, C., and Li, Z., J. Exp. Biol., 2013, vol. 216, pp. 1786–1792.

    Article  CAS  PubMed  Google Scholar 

  3. Li, X.L., Zhang, C.L., Fang, W.H., and Lin, F.C., J. Zhejiang. Univ. Sci. B, 2008, vol. 9, pp. 578–581.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  4. Huang, C.H., Lin, W.Y., and Chu, J.H., Comp. Biochem. Physiol. A Mol. Integr. Physiol., 2005, vol. 142, pp. 383–388.

    Article  PubMed  Google Scholar 

  5. Cloonan, N., Wani, S., Xu, Q., Gu, J., Lea, K., Heater, S., Barbacioru, C., Steptoe, A.L., Martin, H.C., Nourbakhsh, E., Krishnan, K., Gardiner, B., Wang, X., Nones, K., Steen, J.A., Matigian, N.A., Wood, D.L., Kassahn, K.S., Waddell, N., Shepherd, J., Lee, C., Ichikawa, J., McKernan, K., Bramlett, K., Kuersten, S., and Grimmond, S.M., Genome. Biol., 2011, vol. 12, p. R126.

  6. Turner, M.L., Schnorfeil, F.M., and Brocker, T., J. Immunol., 2011, vol. 187, pp. 3911–3917.

    Article  CAS  PubMed  Google Scholar 

  7. Connelly, C.M., and Deiters, A., Methods Mol. Biol., 2014, vol. 1095, pp. 147–156.

    Article  CAS  PubMed  Google Scholar 

  8. Motameny, S., Wolters, S., Nurnberg, P., and Schumacher, B., Genes (Basel), 2010, vol. 1, pp. 70–84.

    Article  CAS  Google Scholar 

  9. Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A., and Enright, A.J., Nucleic Acids Res., 2006, vol. 34, pp. D140–D144.

  10. Krol, J., Loedige, I., and Filipowicz, W., Nat. Rev. Genet., 2010, vol. 11, pp. 597–610.

    CAS  PubMed  Google Scholar 

  11. Treiber, T., Treiber, N., and Meister, G., Thromb. Haemost., 2012, vol. 107, pp. 605–610.

    Article  CAS  PubMed  Google Scholar 

  12. Bartel, D.P., Cell, 2004, vol. 116, pp. 281–297.

    Article  CAS  PubMed  Google Scholar 

  13. Carrington, J.C., and Ambros, V., Science, 2003, vol. 301, pp. 336–338.

    Article  CAS  PubMed  Google Scholar 

  14. Huang, Y., Shen, X.J., Zou, Q., Wang, S.P., Tang, S.M., and Zhang, G.Z., J. Physiol. Biochem., 2011, vol. 67, pp. 129–139.

    Article  CAS  PubMed  Google Scholar 

  15. Smibert, P., and Lai, E.C., Semin. Cell Dev. Biol., 2010, vol. 21, pp. 745–753.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  16. Dorner, S., Eulalio, A., Huntzinger, E., and Izaurralde, E., EMBO Rep., 2007, vol. 8, pp. 723–729.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  17. Bidarimath, M., Khalaj, K., Wessels, J.M., and Tayade, C., Cell. Mol. Immunol., 2014, vol. 11, pp. 538–547.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  18. Ferreira, D.M., Simao, A.L., Rodrigues, C.M., and Castro, R.E., FEBS J., 2014, vol. 281, pp. 2503–2524.

    Article  CAS  PubMed  Google Scholar 

  19. Pedersen, I.M., Cheng, G., Wieland, S., Volinia, S., Croce, C.M., Chisari, F.V., and David, M., Nature, 2007, vol. 449, pp. 919–922.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  20. Zhang, W., Zhou, X., and Xia, J., Methods Mol. Biol., 2012, vol. 883, pp. 221–227.

    Article  CAS  PubMed  Google Scholar 

  21. Mi, X., Wei, Z., Zhou, Z., and Liu, X., Comp. Biochem. Physiol. Part D Genomics Proteomics, 2014, vol. 10, pp. 1–8.

    Article  CAS  PubMed  Google Scholar 

  22. Han, J., Li, A., Liu, H., Wen, X., Zhao, M., Korir, N.B., Korir, N.K., Wang, C., and Fang, J., Gene, 2014, vol. 536, pp. 151–162.

    Article  CAS  PubMed  Google Scholar 

  23. Zhang, W., Luo, Y., Gong, X., Zeng, W., and Li, S., Comput. Biol. Chem., 2009, vol. 33, pp. 84–93.

    Article  CAS  PubMed  Google Scholar 

  24. Yoon, S. and De Micheli, G., Birth Defects Res. C Embryo Today, 2006, vol. 78, pp. 118–128.

    Article  CAS  PubMed  Google Scholar 

  25. Takada, S., Berezikov, E., Yamashita, Y., Lagos-Quintana, M., Kloosterman, W. P., Enomoto, M., Hatanaka, H., Fujiwara, S., Watanabe, H., Soda, M., Choi, Y. L., Plasterk, R.H., Cuppen, E., and Mano, H., Nucleic Acids Res., 2006, vol. 34, p. e115.

  26. Jagadeeswaran, G., Zheng, Y., Li, Y.F., Shukla, L.I., Matts, J., Hoyt, P., Macmil, S.L., Wiley, G.B., Roe, B.A., Zhang, W., and Sunkar, R., New Phytol., 2009, vol. 184, pp. 85–98.

    Article  CAS  PubMed  Google Scholar 

  27. Stowe, H.M., Curry, E., Calcatera, S.M., Krisher, R.L., Paczkowski, M., and Pratt, S.L., Gene, 2012, vol. 501, pp. 198–205.

    Article  CAS  PubMed  Google Scholar 

  28. Huang, Y., Zou, Q., Sun, X.H., and Zhao, L.P., Appl. Biochem. Biotechnol., 2014, vol. 173, pp. 1011–1022.

    Article  CAS  PubMed  Google Scholar 

  29. Xiang, J., Cheng, A., Wang, M., Zhang, S., Zhu, D., Jia, R., Chen, S., Zhou, Y., Wang, X., and Chen, X., Virol. J., 2012, vol. 9, p. 93.

  30. Keshavan, R., Virata, M., Keshavan, A., and Zeller, R.W., Zoolog. Sci., 2010, vol. 27, pp. 162–170.

    Article  CAS  PubMed  Google Scholar 

  31. Thiebaut, F., Grativol, C., Carnavale-Bottino, M., Rojas, C.A., Tanurdzic, M., Farinelli, L., Martienssen, R.A., Hemerly, A.S., and Ferreira, P.C., BMC Genomics, vol. 2012, vol. 13, p. 290.

  32. Reshmi, G., Chandra, S.S., Babu, V.J., Babu, P.S., Santhi, W.S., Ramachandran, S., Lakshmi, S., Nair, A.S., and Pillai, M.R., Genomics, 2011, vol. 97, pp. 333–340.

    Article  CAS  PubMed  Google Scholar 

  33. Dong, Q.H., Han, J., Yu, H.P., Wang, C., Zhao, M.Z., Liu, H., Ge, A.J., and Fang, J.G., J. Hered., 2012, vol. 103, pp. 268–277.

    Article  CAS  PubMed  Google Scholar 

  34. Galla, G., Volpato, M., Sharbel, T.F., and Barcaccia, G., Plant Reprod., 2013, vol. 26, pp. 209–229.

    Article  CAS  PubMed  Google Scholar 

  35. Akter, A., Islam, M.M., Mondal, S.I., Mahmud, Z., Jewel, N.A., Ferdous, S., Amin, M.R., and Rahman, M.M., Saudi J. Biol. Sci., 2014, vol. 21, pp. 3–12.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  36. Jones-Rhoades, M.W. and Bartel, D.P., Mol. Cell, 2004, vol. 14, pp. 787–799.

    Article  CAS  PubMed  Google Scholar 

  37. Sunkar, R. and Jagadeeswaran, G., BMC Plant Biol., 2008, vol. 8, p. 37.

  38. Dezulian, T., Remmert, M., Palatnik, J.F., Weigel, D., and Huson, D.H., Bioinformatics, 2006, vol. 22, pp. 359–360.

    Article  CAS  PubMed  Google Scholar 

  39. Xu, J.H., Li, F., and Sun, Q.F., Genomics Proteomics Bioinformatics, 2008, vol. 6, pp. 121–128.

    Article  CAS  PubMed  Google Scholar 

  40. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S., Mol. Biol. Evol., 2011, vol. 28, pp. 2731–2739.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  41. Saitou, N. and Nei, M., Mol. Biol. Evol., 1987, vol. 4, pp. 406–425.

    CAS  PubMed  Google Scholar 

  42. Mohammadi-Yeganeh, S., Paryan, M., Mirab Samiee, S., Soleimani, M., Arefian, E., Azadmanesh, K., Mostafavi, E., Mahdian, R., and Karimipoor, M., Mol. Biol. Rep., 2013, vol. 40, pp. 3665–3674.

    Article  CAS  PubMed  Google Scholar 

  43. Chen, C., Ridzon, D.A., Broomer, A.J., Zhou, Z., Lee, D.H., Nguyen, J.T., Barbisin, M., Xu, N.L., Mahuvakar, V.R., Andersen, M.R., Lao, K.Q., Livak, K.J., and Guegler, K.J., Nucleic Acids Res., 2005, vol. 33, p. e179.

  44. Varkonyi-Gasic, E. and Hellens, R.P., Methods Mol. Biol., 2011, vol. 744, pp. 145–157.

    Article  CAS  PubMed  Google Scholar 

  45. Rehmsmeier, M., Steffen, P., Hochsmann, M., and Giegerich, R., RNA, 2004, vol. 10, pp. 1507–1517.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  46. Wang, Z., Pascual-Anaya, J., Zadissa, A., Li, W., Niimura, Y., Huang, Z., Li, C., White, S., Xiong, Z., Fang, D., Wang, B., Ming, Y., Chen, Y., Zheng, Y., Kuraku, S., Pignatelli, M., Herrero, J., Beal, K., Nozawa, M., Li, Q., Wang, J., Zhang, H., Yu, L., Shigenobu, S., Liu, J., Flicek, P., Searle, S., Kuratani, S., Yin, Y., Aken, B., Zhang, G., and Irie, N., Nat. Genet., 2013, vol. 45, pp. 701–706.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  47. Zhang, B., Pan, X., Cannon, C.H., Cobb, G.P., and Anderson, T.A., Plant J., 2006, vol. 46, pp. 243–259.

    Article  CAS  PubMed  Google Scholar 

  48. Gong, P., Xie, F., Zhang, B., and Perkins, E.J., Comput. Biol. Chem., 2010, vol. 34, pp. 313–319.

    Article  CAS  PubMed  Google Scholar 

  49. Zhang, B., Stellwag, E.J., and Pan, X., Gene, 2009, vol. 443, pp. 100–109.

    Article  CAS  PubMed  Google Scholar 

  50. Xie, S.S., Huang, T.H., Shen, Y., Li, X.Y., Zhang, X.X., Zhu, M.J., Qin, H.Y., and Zhao, S.H., Anim. Genet., 2010, vol. 41, pp. 179–190.

    Article  CAS  PubMed  Google Scholar 

  51. Liu, X., Luo, G., Bai, X., and Wang, X.J., J. Genet. Genomics, 2009, vol. 36, pp. 591–601.

    Article  CAS  PubMed  Google Scholar 

  52. Shomron, N., Golan, D., and Hornstein, E., J. Biomed. Biotechnol., 2009, vol. 2009, p. 594738.

  53. Christodoulou, F., Raible, F., Tomer, R., Simakov, O., Trachana, K., Klaus, S., Snyman, H., Hannon, G.J., Bork, P., and Arendt, D., Nature, 2010, vol. 463, pp. 1084–1088.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  54. Delfino, K.R., and Rodriguez-Zas, S.L., PLoS One, 2013, vol. 8, p. e58608.

  55. Linhart, C., Halperin, Y., and Shamir, R., Genome Res., 2008, vol. 18, pp. 1180–1189.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  56. Zhao, L., Lu, X., and Cao, Y., Cell Signal., 2013, vol. 25, pp. 1625–1634.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  57. Inui, M., Martello, G., and Piccolo, S., Nat. Rev. Mol. Cell. Biol., 2010, vol. 11, pp. 252–263.

    Article  CAS  PubMed  Google Scholar 

  58. Lynn, F.C., Trends Endocrinol. Metab., 2009, vol. 20, pp. 452–459.

    Article  CAS  PubMed  Google Scholar 

  59. Ramirez, C.M., Rotllan, N., Vlassov, A.V., Davalos, A., Li, M., Goedeke, L., Aranda, J.F., Cirera-Salinas, D., Araldi, E., Salerno, A., Wanschel, A., Zavadil, J., Castrillo, A., Kim, J., Suarez, Y., and Fernandez-Hernando, C., Circ. Res., 2013, vol. 112, pp. 1592–1601.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  60. Chaudhuri, K., and Chatterjee, R., DNA Cell. Biol., 2007, vol. 26, pp. 321–337.

    Article  CAS  PubMed  Google Scholar 

  61. Hamzeiy, H., Allmer, J., and Yousef, M., Methods Mol. Biol., 2014, vol. 1107, pp. 207–221.

    Article  CAS  PubMed  Google Scholar 

  62. Ritchie, W., Rasko, J.E., and Flamant, S., Adv. Exp. Med. Biol., 2013, vol. 774, pp. 39–53.

    Article  CAS  PubMed  Google Scholar 

  63. Pirkkala, L., Nykanen, P., and Sistonen, L., FASEB J., 2001, vol. 15, pp. 1118–1131.

    Article  CAS  PubMed  Google Scholar 

  64. Li, X.L., Kang, Y., Zhang, X.Y., Zhu, B.L., and Fang, W.H., J. Zhejiang Univ. Sci. B., 2012, vol. 13, pp. 465–477.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Animal Science and Technology College, Henan University of Science and Technology, Luoyang City, Henan Province, 471003, PR China

    Yong Huang, Hong Tao Ren, Zhan Bin Wang & Xi Hong Sun

Authors
  1. Yong Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hong Tao Ren
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zhan Bin Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xi Hong Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xi Hong Sun.

Additional information

The article is published in the original.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Huang, Y., Ren, H.T., Wang, Z.B. et al. Identification and validation of novel microrna molecule from the Pelodiscus sinensis by bioinformatics approaches. Russ J Bioorg Chem 41, 368–378 (2015). https://doi.org/10.1134/S1068162015040147

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1068162015040147

Keywords

Search

Navigation