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.
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Abbreviations
- GO analysis:
-
gene ontology enrichment analysis
- KEGG analysis:
-
Kyoto Encyclopedia of Genes and Genomes pathway analysis
- miRNA:
-
microRNA
References
Bartel, D. P. (2009) MicroRNAs: target recognition and regulatory functions, Cell, 136, 215–233.
Chekulaeva, M., and Filipowicz, W. (2009) Mechanisms of miRNA-mediated post-transcriptional regulation in ani-mal cells, Curr. Opin. Cell Biol., 21, 452–460.
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.
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.
Tang, G. (2005) siRNA and miRNA: an insight into RISCs, Trends Biochem. Sci., 30, 106–114.
Shukla, G. C., Singh, J., and Barik, S. (2011) MicroRNAs: processing, maturation, target recognition and regulatory functions, Mol. Cell Pharmacol., 3, 83–92.
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.
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.
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.
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.
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.
Gao, K. Q., and Shubin, N. H. (2003) Earliest known crown-group salamanders, Nature, 422, 424–428.
Gao, K. Q., and Shubin, N. H. (2001) Late Jurassic sala-manders from Northern China, Nature, 410, 574–577.
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.
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.
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.
Simmaco, M., Mignogna, G., and Barra, D. (1998) Antimicrobial peptides from amphibian skin: what do they tell us? Biopolymers, 47, 435–450.
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.
Chen, R., Du, J., Ma, L., Wang, L. Q., **e, 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.
Huang, Y., Ren, H. T., **ong, 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.
Huang, Y., Gao, X. C., **ong, 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.
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.
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.
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.
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.
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.
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.
Ji, Z., Wang, G., **e, 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.
Ambady, S., Wu, Z., and Dominko, T. (2012) Identification of novel microRNAs in Xenopus laevis metaphase II arrest-ed eggs, Genesis, 50, 286–299.
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.
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.
Roush, S., and Slack, F. J. (2008) The let-7 family of microRNAs, Trends Cell Biol., 18, 505–516.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Andreassen, R., and Hoyheim, B. (2017) miRNAs associ-ated with immune response in teleost fish, Dev. Comp. Immunol., 75, 77–85.
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.
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.
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.
Gantier, M. P. (2010) New perspectives in microRNA reg-ulation of innate immunity, J. Interferon Cytokine Res., 30, 283–289.
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Originally published in Biochemistry (Moscow) On-Line Papers in Press, as Manuscript BM17-498, March 26, 2018.
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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
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DOI: https://doi.org/10.1134/S0006297918060147