Skip to main content
SpringerLink
Log in

Identification and Characterization of MicroRNAs in Skin of Chinese Giant Salamander (Andrias davidianus) by the Deep Sequencing Approach

  • Published:
Biochemistry (Moscow) Aims and scope Submit manuscript

Abstract

MicroRNAs (miRNA) play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. However, the miRNAs from skin of Andrias davidianus have not been reported. In this study, a small-RNA cDNA library was constructed and sequenced from skin of A. davidianus. A total of 513 conserved miRNAs belonging to 174 families were identified. The remaining 108 miRNAs we identified were novel and likely to be skin tissue-specific but were expressed at low levels. The presence of randomly selected 15 miRNAs identified and their expression in eight different tissues from A. davidianus were validated by stem-loop qRT-PCR. For better understanding the functions of miRNAs, 129,791 predicated target genes were analyzed by GO and their pathways illustrated by KEGG pathway analyses. The results show that these identified miRNAs from A. davidianus skin are involved in a broad range of physiological functions including metabolism, growth, development, and immune responses. This study exhaustively identifies miRNAs and their target genes, which will ultimately pave the way for understanding their role in skin of A. davidianus and other amphibians. Further studies are necessary to better understand miRNA-mediated gene regulation.

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

Abbreviations

GO analysis:

gene ontology enrichment analysis

KEGG analysis:

Kyoto Encyclopedia of Genes and Genomes pathway analysis

miRNA:

microRNA

References

  1. Bartel, D. P. (2009) MicroRNAs: target recognition and regulatory functions, Cell, 136, 215–233.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  2. Chekulaeva, M., and Filipowicz, W. (2009) Mechanisms of miRNA-mediated post-transcriptional regulation in ani-mal cells, Curr. Opin. Cell Biol., 21, 452–460.

    Article  PubMed  CAS  Google Scholar 

  3. Johanson, T. M., Lew, A. M., and Chong, M. M. (2013) MicroRNA-independent roles of the RNase III enzymes Drosha and Dicer, Open Biol., 3, 130144.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  4. Gregory, R. I., Chendrimada, T. P., Cooch, N., and Shiekhattar, R. (2005) Human RISC couples microRNA biogenesis and posttranscriptional gene silencing, Cell, 123, 631–640.

    Article  PubMed  CAS  Google Scholar 

  5. Tang, G. (2005) siRNA and miRNA: an insight into RISCs, Trends Biochem. Sci., 30, 106–114.

    Article  PubMed  CAS  Google Scholar 

  6. Shukla, G. C., Singh, J., and Barik, S. (2011) MicroRNAs: processing, maturation, target recognition and regulatory functions, Mol. Cell Pharmacol., 3, 83–92.

    PubMed  PubMed Central  CAS  Google Scholar 

  7. Huang, Y., Shen, X. J., Zou, Q., Wang, S. P., Tang, S. M., and Zhang, G. Z. (2011) Biological functions of microRNAs: a review, J. Physiol. Biochem., 67, 129–139.

    Article  PubMed  CAS  Google Scholar 

  8. Shi, C., Zhang, X., Li, X., Zhang, L., Li, L., Sun, Z., Fu, X., Wu, J., Chang, Y., Li, W., Chen, Q., and Zhang, M. (2016) Effects of microRNA-21 on the biological functions of T-cell acute lymphoblastic lymphoma/leukemia, Oncol. Lett., 12, 4173–4180.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. Wang, L., Li, G., Yao, Z. Q., Moorman, J. P., and Ning, S. (2015) MicroRNA regulation of viral immunity, latency, and carcinogenesis of selected tumor viruses and HIV, Rev. Med. Virol., 25, 320–341.

    Article  PubMed  CAS  Google Scholar 

  10. Martin, R. C., Liu, P. P., Goloviznina, N. A., and Nonogaki, H. (2010) MicroRNA, seeds, and Darwin?: diverse function of miRNA in seed biology and plant responses to stress, J. Exp. Bot., 61, 2229–2234.

    Article  PubMed  CAS  Google Scholar 

  11. Murphy, R. W., Fu, J., Upton, D. E., de Lema, T., and Zhao, E. M. (2000) Genetic variability among endangered Chinese giant salamanders, Andrias davidianus, Mol. Ecol., 9, 1539–1547.

    Article  PubMed  CAS  Google Scholar 

  12. Gao, K. Q., and Shubin, N. H. (2003) Earliest known crown-group salamanders, Nature, 422, 424–428.

    Article  PubMed  CAS  Google Scholar 

  13. Gao, K. Q., and Shubin, N. H. (2001) Late Jurassic sala-manders from Northern China, Nature, 410, 574–577.

    Article  PubMed  CAS  Google Scholar 

  14. Huang, Y., Yang, Y. B., Gao, X. C., Ren, H. T., and Sun, X. H. (2017) Identification and characterization of the Chinese giant salamander (Andrias davidianus) miRNAs by deep sequencing and predication of their targets, 3 Biotech., 7, 235.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Pounds, J. A., Bustamante, M. R., Coloma, L. A., Consuegra, J. A., Fogden, M. P., Foster, P. N., La Marca, E., Masters, K. L., Merino-Viteri, A., Puschendorf, R., Ron, S. R., Sa’nchez-Azofeifa, G. A., Still, C. J., and Young, B. E. (2006) Widespread amphibian extinctions from epidemic disease driven by global warming, Nature, 439, 161–167.

    Article  PubMed  CAS  Google Scholar 

  16. Fisher, M. C., Henk, D. A., Briggs, C. J., Brownstein, J. S., Madoff, L. C., McCraw, S. L., and Gurr, S. J. (2012) Emerging fungal threats to animal, plant and ecosystem health, Nature, 484, 186–194.

    Article  PubMed  CAS  Google Scholar 

  17. Simmaco, M., Mignogna, G., and Barra, D. (1998) Antimicrobial peptides from amphibian skin: what do they tell us? Biopolymers, 47, 435–450.

    Article  PubMed  CAS  Google Scholar 

  18. Li, F., Wang, L., Lan, Q., Yang, H., Li, Y., Liu, X., and Yang, Z. (2015) RNA-Seq analysis and gene discovery of Andrias davidianus using Illumina short read sequencing, PLoS One, 10, e0123730.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Chen, R., Du, J., Ma, L., Wang, L. Q., Xie, S. S., Yang, C. M., Lan, X. Y., Pan, C. Y., and Dong, W. Z. (2017) Comparative microRNAome analysis of the testis and ovary of the Chinese giant salamander, Reproduction, 154, 169–179.

    Article  PubMed  Google Scholar 

  20. Huang, Y., Ren, H. T., Xiong, J. L., Gao, X. C., and Sun, X. H. (2017) Identification and characterization of known and novel microRNAs in three tissues of Chinese giant salamander base on deep sequencing approach, Genomics, 109, 258–264.

    Article  PubMed  CAS  Google Scholar 

  21. Huang, Y., Gao, X. C., Xiong, J. L., Ren, H. T., and Sun, X. H. (2017) Sequencing and de novo transcriptome assem-bly of the Chinese giant salamander (Andrias davidianus), Genom. Data, 12, 109–110.

    Article  PubMed  PubMed Central  Google Scholar 

  22. Hurley, J., Roberts, D., Bond, A., Keys, D., and Chen, C. (2012) Stem-loop RT-qPCR for microRNA expression profiling, Methods Mol. Biol., 822, 33–52.

    Article  PubMed  CAS  Google Scholar 

  23. Yang, L. H., Wang, S. L., Tang, L. L., Liu, B., Ye, W. L., Wang, L. L., Wang, Z. Y., Zhou, M. T., and Chen, B. C. (2014) Universal stem-loop primer method for screening and quantification of microRNA, PLoS One, 9, e115293.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  24. Huang, Y., Cheng, J. H., Luo, F. N., Pan, H., Sun, X. J., Diao, L. Y., and Qin, X. J. (2016) Genome-wide identifica-tion and characterization of microRNA genes and their tar-gets in large yellow croaker (Larimichthys crocea), Gene, 576, 261–267.

    Article  PubMed  CAS  Google Scholar 

  25. Sun, J., Zhang, B., Lan, X., Zhang, C., Lei, C., and Chen, H. (2014) Comparative transcriptome analysis reveals sig-nificant differences in microRNA expression and their tar-get genes between adipose and muscular tissues in cattle, PLoS One, 9, e102142.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  26. Fu, Y., Shi, Z., Wu, M., Zhang, J., Jia, L., and Chen, X. (2011) Identification and differential expression of microRNAs during metamorphosis of the Japanese floun-der (Paralichthys olivaceus), PLoS One, 6, e22957.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  27. Yu, X., Zhou, Q., Cai, Y., Luo, Q., Lin, H., Hu, S., and Yu, J. (2009) A discovery of novel microRNAs in the silkworm (Bombyx mori) genome, Genomics, 94, 438–444.

    Article  PubMed  CAS  Google Scholar 

  28. Ji, Z., Wang, G., Xie, Z., Zhang, C., and Wang, J. (2012) Identification and characterization of microRNA in the dairy goat (Capra hircus) mammary gland by Solexa deep-sequencing technology, Mol. Biol. Rep., 39, 9361–9371.

    Article  PubMed  CAS  Google Scholar 

  29. Ambady, S., Wu, Z., and Dominko, T. (2012) Identification of novel microRNAs in Xenopus laevis metaphase II arrest-ed eggs, Genesis, 50, 286–299.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  30. Sun, G. R., Li, M., Li, G. X., Tian, Y. D., Han, R. L., and Kang, X. T. (2012) Identification and abundance of miRNA in chicken hypothalamus tissue determined by Solexa sequencing, Genet. Mol. Res., 11, 4682–4694.

    Article  PubMed  CAS  Google Scholar 

  31. Reinhart, B. J., Slack, F. J., Basson, M., Pasquinelli, A. E., Bettinger, J. C., Rougvie, A. E., Horvitz, H. R., and Ruvkun, G. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans, Nature, 403, 901–906.

    Article  PubMed  CAS  Google Scholar 

  32. Roush, S., and Slack, F. J. (2008) The let-7 family of microRNAs, Trends Cell Biol., 18, 505–516.

    Article  PubMed  CAS  Google Scholar 

  33. Lehmann, S. M., Kruger, C., Park, B., Derkow, K., Rosenberger, K., Baumgart, J., Trimbuch, T., Eom, G., Hinz, M., Kaul, D., Habbel, P., Kaelin, R., Franzoni, E., Rybak, A., Nguyen, D., Veh, R., Ninnemann, O., Peters, O., Nitsch, R., Heppner, F. L., Golenbock, D., Schott, E., Ploegh, H. L., Wulczyn, F. G., and Lehnardt, S. (2012) An unconventional role for miRNA: let-7 activates Toll-like receptor 7 and causes neurodegeneration, Nat. Neurosci., 15, 827–835.

    Article  PubMed  CAS  Google Scholar 

  34. Frost, R. J., and Olson, E. N. (2011) Control of glucose homeostasis and insulin sensitivity by the let-7 family of microRNAs, Proc. Natl. Acad. Sci. USA, 108, 21075–21080.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Toledano, H., D’Alterio, C., Czech, B., Levine, E., and Jones, D. L. (2012) The let-7-Imp axis regulates ageing of the Drosophila testis stem-cell niche, Nature, 485, 605–610.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  36. Zhu, H., Shyh-Chang, N., Segre, A. V., Shinoda, G., Shah, S. P., Einhorn, W. S., Takeuchi, A., Engreitz, J. M., Hagan, J. P., Kharas, M. G., Urbach, A., Thornton, J. E., Triboulet, R., Gregory, R. I., DIAGRAM Consortium, MAGIC Investigators, Altshuler, D., and Daley, G. Q. (2011) The Lin28/let-7 axis regulates glucose metabolism, Cell, 147, 81–94.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  37. Su, J. L., Chen, P. S., Johansson, G., and Kuo, M. L. (2012) Function and regulation of let-7 family microRNAs, MicroRNA, 1, 34–39.

    Article  PubMed  CAS  Google Scholar 

  38. Mondol, V., and Pasquinelli, A. E. (2012) Let’s make it happen: the role of let-7 microRNA in development, Curr. Top. Dev. Biol., 99, 1–30.

    Article  PubMed  CAS  Google Scholar 

  39. Wang, X., Cao, L., Wang, Y., Liu, N., and You, Y. (2012) Regulation of let-7 and its target oncogenes (review), Oncol. Lett., 3, 955–960.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  40. Swaminathan, S., Suzuki, K., Seddiki, N., Kaplan, W., Cowley, M. J., Hood, C. L., Clancy, J. L., Murray, D. D., Mendez, C., Gelgor, L., Anderson, B., Roth, N., Cooper, D. A., and Kelleher, A. D. (2012) Differential regulation of the let-7 family of microRNAs in CD4+ T cells alters IL-10 expression, J. Immunol., 188, 6238–6246.

    Article  PubMed  CAS  Google Scholar 

  41. Lin, L., Gan, H., Zhang, H., Tang, W., Sun, Y., Tang, X., Kong, D., Zhou, J., Wang, Y., and Zhu, Y. (2014) MicroRNA21 inhibits SMAD7 expression through a target sequence in the 3′ untranslated region and inhibits prolifer-ation of renal tubular epithelial cells, Mol. Med. Rep., 10, 707–712.

    Article  PubMed  CAS  Google Scholar 

  42. Forster, S. C., Tate, M. D., and Hertzog, P. J. (2015) MicroRNA as type I interferon-regulated transcripts and modulators of the innate immune response, Front. Immunol., 6, 334.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  43. Zhou, R., O’Hara, S. P., and Chen, X. M. (2011) MicroRNA regulation of innate immune responses in epithelial cells, Cell. Mol. Immunol., 8, 371–379.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Andreassen, R., and Hoyheim, B. (2017) miRNAs associ-ated with immune response in teleost fish, Dev. Comp. Immunol., 75, 77–85.

    Article  PubMed  CAS  Google Scholar 

  45. Chen, X., Li, Q., Wang, J., Guo, X., Jiang, X., Ren, Z., Weng, C., Sun, G., Wang, X., Liu, Y., Ma, L., Chen, J. Y., Wang, J., Zen, K., Zhang, J., and Zhang, C. Y. (2009) Identification and characterization of novel amphioxus microRNAs by Solexa sequencing, Genome Biol., 10, R78.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  46. Zhang, B. H., Pan, X. P., Cox, S. B., Cobb, G. P., and Anderson, T. A. (2006) Evidence that miRNAs are different from other RNAs, Cell. Mol. Life Sci., 63, 246–254.

    Article  PubMed  CAS  Google Scholar 

  47. Huang, L., Yin, Z. J., Feng, Y. F., Zhang, X. D., Wu, T., Ding, Y. Y., Ye, P. F., Fu, K., and Zhang, M. Q. (2016) Identification and differential expression of microRNAs in the ovaries of pigs (Sus scrofa) with high and low litter sizes, Anim. Genet., 47, 543–551.

    Article  PubMed  CAS  Google Scholar 

  48. Gantier, M. P. (2010) New perspectives in microRNA reg-ulation of innate immunity, J. Interferon Cytokine Res., 30, 283–289.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. College of Animal Science and Technology, Henan University of Science and Technology, 471023, Luoyang, China

    Yong Huang

  2. Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China

    Wang Bao Gong

Authors
  1. Yong Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wang Bao Gong
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yong Huang.

Additional information

Originally published in Biochemistry (Moscow) On-Line Papers in Press, as Manuscript BM17-498, March 26, 2018.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Huang, Y., Gong, W.B. Identification and Characterization of MicroRNAs in Skin of Chinese Giant Salamander (Andrias davidianus) by the Deep Sequencing Approach. Biochemistry Moscow 83, 766–777 (2018). https://doi.org/10.1134/S0006297918060147

Download citation

  • Received:

  • Revised:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0006297918060147

Keywords

Search

Navigation