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Genomic Analysis of miR-21-3p and Expression Pattern with Target Gene in Olive Flounder

  • Jo, Ara (Department of Biological Sciences, College of Natural Sciences, Pusan National University) ;
  • Lee, Hee-Eun (Department of Biological Sciences, College of Natural Sciences, Pusan National University) ;
  • Kim, Heui-Soo (Department of Biological Sciences, College of Natural Sciences, Pusan National University)
  • Received : 2017.07.31
  • Accepted : 2017.08.15
  • Published : 2017.09.30

Abstract

MicroRNAs (miRNAs) act as regulators of gene expression by binding to the 3' untranslated region (UTR) of target genes. They perform important biological functions in the various species. Among many miRNAs, miR-21-3p is known to serve vital functions in development and apoptosis in olive flounder. Using genomic and bioinformatic tools, evolutionary conservation of miR-21-3p was examined in various species, and expression pattern was analyzed in olive flounder. Conserved sequences (5'-CAGUCG-3') in numerous species were detected through the stem-loop structure of miR-21-3p. Thus, we analyzed target genes of miR-21-3p. Among them, 3' UTR region of PPIL2 gene indicated the highest binding affinity with miR-21-3p based on the minimum free energy value. The PPIL2 gene showed high expression levels in testis tissue of the olive flounder, whereas miR-21-3p showed rather ubiquitous expression patterns except in testis tissue, indicating that miR-21-3p seems to control the PPIL2 gene expression in a complementary repression manner in various tissues of olive flounder. Taken together, this current study contributes to infer the target gene candidates for the miR-21-3p using bioinformatics tools. Furthermore, our data offers important information on the relationship between miR-21-3p and target gene for further functional study.

Keywords

References

  1. Muinos-Gimeno M, Guidi M, Kagerbauer B, Martin-Santos R, Navines R, Alonso P, et al. Allele variants in functional MicroRNA target sites of the neurotrophin-3 receptor gene (NTRK3) as susceptibility factors for anxiety disorders. Hum Mutat 2009;30:1062-1071. https://doi.org/10.1002/humu.21005
  2. Yang P, Tang R, Zhu J, Zou L, Wu R, Zhou H, et al. A functional variant at miR-24 binding site in B7-H2 alters susceptibility to gastric cancer in a Chinese Han population. Mol Immunol 2013;56:98-103. https://doi.org/10.1016/j.molimm.2013.04.010
  3. Minguzzi S, Selcuklu SD, Spillane C, Parle-McDermott A. An NTD-associated polymorphism in the 3' UTR of MTHFD1L can affect disease risk by altering miRNA binding. Hum Mutat 2014;35:96-104. https://doi.org/10.1002/humu.22459
  4. Maxwell EK, Campbell JD, Spira A, Baxevanis AD. Submi-Rine: assessing variants in microRNA targets using clinical genomic data sets. Nucleic Acids Res 2015;43:3886-3898. https://doi.org/10.1093/nar/gkv256
  5. O'Carroll D, Schaefer A. General principals of miRNA biogenesis and regulation in the brain. Neuropsychopharmacology 2013;38:39-54. https://doi.org/10.1038/npp.2012.87
  6. Lee SY, Choi JE, Jeon HS, Hong MJ, Choi YY, Kang HG, et al. A genetic variation in microRNA target site of KRT81 gene is associated with survival in early-stage non-small-cell lung cancer. Ann Oncol 2015;26:1142-1148. https://doi.org/10.1093/annonc/mdv100
  7. Schoof CR, Botelho EL, Izzotti A, Vasques Ldos R. MicroRNAs in cancer treatment and prognosis. Am J Cancer Res 2012;2:414-433.
  8. Gawantka V, Pollet N, Delius H, Vingron M, Pfister R, Nitsch R, et al. Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning. Mech Dev 1998;77:95-141. https://doi.org/10.1016/S0925-4773(98)00115-4
  9. Han HJ, Kim DH, Lee DC, Kim SM, Park SI. Pathogenicity of Edwardsiella tarda to olive flounder, Paralichthys olivaceus (Temminck & Schlegel). J Fish Dis 2006;29:601-609. https://doi.org/10.1111/j.1365-2761.2006.00754.x
  10. Wang HR, Hu YH, Zhang WW, Sun L. Construction of an attenuated Pseudomonas fluorescens strain and evaluation of its potential as a cross-protective vaccine. Vaccine 2009;27:4047-4055. https://doi.org/10.1016/j.vaccine.2009.04.023
  11. Nho SW, Shin GW, Park SB, Jang HB, Cha IS, Ha MA, et al. Phenotypic characteristics of Streptococcus iniae and Streptococcus parauberis isolated from olive flounder (Paralichthys olivaceus). FEMS Microbiol Lett 2009;293:20-27. https://doi.org/10.1111/j.1574-6968.2009.01491.x
  12. Dunham RA. Aquaculture and Fisheries Biotechnology: Genetic Approaches. Wallingford: CABI Publishing, 2004.
  13. Kim WJ, Kim KK, Han HS, Nam BH, Kim YO, Kong HJ, et al. Population structure of the olive flounder (Paralichthys olivaceus) in Korea inferred from microsatellite marker analysis. J Fish Biol 2010;76:1958-1971. https://doi.org/10.1111/j.1095-8649.2010.02638.x
  14. Slatkin M. Gene flow and the geographic structure of natural populations. Science 1987;236:787-792. https://doi.org/10.1126/science.3576198
  15. Zhang C. Novel functions for small RNA molecules. Curr Opin Mol Ther 2009;11:641-651.
  16. Zhang H, Fu Y, Shi Z, Su Y, Zhang J. miR-17 is involved in Japanese Flounder (Paralichthys olivaceus) development by targeting the Cdc42 mRNA. Comp Biochem Physiol B Biochem Mol Biol 2016;191:163-170. https://doi.org/10.1016/j.cbpb.2015.10.005
  17. Fu Y, Shi Z, Wang G, Zhang J, Li W, Jia L. Expression of let-7 microRNAs that are involved in Japanese flounder (Paralichthys olivaceus) metamorphosis. Comp Biochem Physiol B Biochem Mol Biol 2013;165:106-113. https://doi.org/10.1016/j.cbpb.2013.03.012
  18. Petrocca F, Visone R, Onelli MR, Shah MH, Nicoloso MS, de Martino I, et al. E2F1-regulated microRNAs impair TGF${\beta}$-dependent cell-cycle arrest and apoptosis in gastric cancer. Cancer Cell 2008;13:272-286. https://doi.org/10.1016/j.ccr.2008.02.013
  19. Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F, et al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A 2006;103:2257-2261. https://doi.org/10.1073/pnas.0510565103
  20. Zhang L, Volinia S, Bonome T, Calin GA, Greshock J, Yang N, et al. Genomic and epigenetic alterations deregulate micro-RNA expression in human epithelial ovarian cancer. Proc Natl Acad Sci U S A 2008;105:7004-7009. https://doi.org/10.1073/pnas.0801615105
  21. Mascellani N, Tagliavini L, Gamberoni G, Rossi S, Marchesini J, Taccioli C, et al. Using miRNA expression data for the study of human cancer. Minerva Biotechnol 2008;20:23-30.
  22. Rath SN, Das D, Konkimalla VB, Pradhan SK. In silico study of miRNA based gene regulation, involved in solid cancer, by the assistance of argonaute protein. Genomics Inform 2016;14: 112-124. https://doi.org/10.5808/GI.2016.14.3.112
  23. Maffioletti E, Cattaneo A, Rosso G, Maina G, Maj C, Gennarelli M, et al. Peripheral whole blood microRNA alterations in major depression and bipolar disorder. J Affect Disord 2016;200:250-258. https://doi.org/10.1016/j.jad.2016.04.021
  24. Jo A, Im J, Lee HE, Jang D, Nam GH, Mishra A, et al. Evolutionary conservation and expression of miR-10a-3p in olive flounder and rock bream. Gene 2017;628:16-23. https://doi.org/10.1016/j.gene.2017.07.020
  25. Wang H, Bei Y, Shen S, Huang P, Shi J, Zhang J, et al. miR-21-3p controls sepsis-associated cardiac dysfunction via regulating SORBS2. J Mol Cell Cardiol 2016;94:43-53. https://doi.org/10.1016/j.yjmcc.2016.03.014
  26. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, et al. A combined computational-experimental approach predicts human microRNA targets. Genes Dev 2004;18:1165-1178. https://doi.org/10.1101/gad.1184704
  27. Cybula M, Wieteska L, Jozefowicz-Korczynska M, Karbownik MS, Grzelczyk WL, Szemraj J. New miRNA expression abnormalities in laryngeal squamous cell carcinoma. Cancer Biomark 2016;16:559-568. https://doi.org/10.3233/CBM-160598
  28. Romay MC, Che N, Becker SN, Pouldar D, Hagopian R, Xiao X, et al. Regulation of NF-${\kappa}B$ signaling by oxidized glycerophospholipid and IL-$1{\beta}$ induced miRs-21-3p and -27a-5p in human aortic endothelial cells. J Lipid Res 2015;56:38-50. https://doi.org/10.1194/jlr.M052670
  29. Zhou XH, Ren YM, Wei ZJ, Lin W, Fan BY, Liu S, et al. Differential expression of miRNAs in Osborne's ligament of cubital tunnel syndrome. Mol Med Rep 2017;16:687-695. https://doi.org/10.3892/mmr.2017.6663
  30. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 2003;115:787-798. https://doi.org/10.1016/S0092-8674(03)01018-3
  31. Hatakeyama S, Yada M, Matsumoto M, Ishida N, Nakayama KI. U box proteins as a new family of ubiquitin-protein ligases. J Biol Chem 2001;276:33111-33120. https://doi.org/10.1074/jbc.M102755200
  32. Pushkarsky T, Yurchenko V, Vanpouille C, Brichacek B, Vaisman I, Hatakeyama S, et al. Cell surface expression of CD147/EMMPRIN is regulated by cyclophilin 60. J Biol Chem 2005;280:27866-27871. https://doi.org/10.1074/jbc.M503770200
  33. Belfiori-Carrasco LF, Marcora MS, Bocai NI, Ceriani MF, Morelli L, Castano EM. A novel genetic screen identifies modifiers of age-dependent amyloid beta toxicity in the Drosophila brain. Front Aging Neurosci 2017;9:61.
  34. Radfar MH, Wong W, Morris Q. Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms. PLoS One 2011;6:e19312. https://doi.org/10.1371/journal.pone.0019312
  35. Chang YY, Kuo WH, Hung JH, Lee CY, Lee YH, Chang YC, et al. Deregulated microRNAs in triple-negative breast cancer revealed by deep sequencing. Mol Cancer 2015;14:36. https://doi.org/10.1186/s12943-015-0301-9
  36. Yaffe MB, Schutkowski M, Shen M, Zhou XZ, Stukenberg PT, Rahfeld JU, et al. Sequence-specific and phosphorylation-dependent proline isomerization: a potential mitotic regulatory mechanism. Science 1997;278:1957-1960. https://doi.org/10.1126/science.278.5345.1957
  37. Ranganathan R, Lu KP, Hunter T, Noel JP. Structural and functional analysis of the mitotic rotamase Pin1 suggests substrate recognition is phosphorylation dependent. Cell 1997;89:875-886. https://doi.org/10.1016/S0092-8674(00)80273-1
  38. Fanghanel J, Akiyama H, Uchida C, Uchida T. Comparative analysis of enzyme activities and mRNA levels of peptidyl prolyl cis/trans isomerases in various organs of wild type and Pin1-/- mice. FEBS Lett 2006;580:3237-3245. https://doi.org/10.1016/j.febslet.2006.04.087

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