Expression regulation of a mature intronic miR3029 by 5′ UTR-like

  • Qingwei Wang
  • Fosheng Li
  • Shuhua Zhu
  • Shenghua Wang
  • Wenguo WangEmail author
  • Yang HeEmail author
Original Article


5′ UTR of the coding gene affected gene expression at the transcription and translation levels. For miRNA, 5′ UTR (termed 5′ UTR-like) is similar to UTR of encoding protein gene. However, the function of 5′ UTR-like has not been reported in the regulation of pre-miRNA formation and the process of miRNA’s formation. In this study, the regulated elements of 5′ UTR-like of intron miR3029 were analyzed by bioinformatics. The function analysis of primary structure of 5′ UTR-like was studied by the transient expression system of Arabidopsis thaliana protoplast. The function of second-structure stem loops of 5′ UTR-like was conducted by detecting the expression of miRNA3029 and pri-miRNA3029 in transgenic tobacco. In this study, we found that 5′ UTR-like region of miR3029 existences low temperature (LTR), oxygen stress element (ARE) and stem loop structure. These elements and structure may control miRNA’s stability and thereby affect the formation of mature miR3029. There also existed a translation enhancer similar to that of the UTRs of coding genes. The function analysis of second structure found that the predicted stem loop 5 can promote the expression of mature miR3029; stem loops 1, 2, 3 and 4 can inhibit the formation of mature miR3029. To sum up, this study lays a foundation for exploring the mechanism of how the primary transcript is cleaved into pre-miRNA, and provides reference for the study of the regulation of miRNA.


5′ UTR-like Intronic miRNA Biogenesis Rice 



Nuclear cap-binding complex


The C2H2 zinc-finger protein SERRATE


The dsRNA-binding protein HYPONASTIC LEAVES1


Untranslational region




Luciferase gene


Precursor miRNA


The primary of miRNA


The open reading frame


Internal ribosome entry site



This research was supported by the National Science Fund of China (Nos. 31070276 and 31270360) and Genetically Modified Organisms Breeding Major Projects (2016ZX08010001-10).

Compliance with ethical standards

Conflict of interest

All of the authors declare that they have no competing interests.

Supplementary material

11738_2018_2713_MOESM1_ESM.doc (97 kb)
Supplementary material 1 (DOC 97 KB)
11738_2018_2713_MOESM2_ESM.doc (40 kb)
Supplementary material 2 (DOC 40 KB)


  1. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297CrossRefPubMedGoogle Scholar
  2. Bugaut A, Balasubramanian S (2012) 5′-UTR RNA G-quadruplexes: translation regulation and targeting. Nucleic Acids Res 40:4727–4741. CrossRefPubMedPubMedCentralGoogle Scholar
  3. Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655. CrossRefPubMedPubMedCentralGoogle Scholar
  4. Chapman EJ, Carrington JC (2007) Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 8:884–896. CrossRefPubMedGoogle Scholar
  5. Czech B, Hannon GJ (2011) Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet 12:19–31. CrossRefPubMedGoogle Scholar
  6. Frolov I, Hardy R, Rice CM (2001) Cis-acting RNA elements at the 5′end of Sindbis virus genome RNA regulate minus-and plus-strand RNA synthesis. RNA 7:1638–1651.doi: 10.1017.S135583820101010XCrossRefPubMedPubMedCentralGoogle Scholar
  7. Gibson SI (2005) Control of plant development and gene expression by sugar signaling. Curr Opin Plant Biol 8:93–102. CrossRefPubMedGoogle Scholar
  8. Gray NK, Hentze MW (1994) Regulation of protein synthesis by mRNA structure. Mol Biol Rep 19:195–200. CrossRefPubMedGoogle Scholar
  9. Gray NK, Wickens M (1998) Control of translation initiation in animals. Ann Rev Cell Dev Biol 14:399–458. CrossRefGoogle Scholar
  10. Hentze MW, Kühn LC (1996) Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. Proc Natl Acad Sci 93:8175–8182CrossRefPubMedGoogle Scholar
  11. ​Horsch RB (1985) A simple and general method for transferring genes into plants. Science 227:1229–1231  CrossRefGoogle Scholar
  12. Kawaguchi R, Bailey-Serres J (2002) Regulation of translational initiation in plants. Curr Opin Plant Biol 5:460–465. CrossRefPubMedGoogle Scholar
  13. Kim VN (2005) MicroRNA biogenesis: coordinated cropping and dicing nature reviews. Mol Cell Biol 6:376–385. CrossRefGoogle Scholar
  14. Klein R, Mullet J (1987) Control of gene expression during higher plant chloroplast biogenesis. Protein synthesis and transcript levels of psbA, psaA-psaB, and rbcL in dark-grown and illuminated barley seedlings. J Biol Chem 262:4341–4348PubMedGoogle Scholar
  15. Kozak M (1987) An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res 15:8125–8148CrossRefPubMedPubMedCentralGoogle Scholar
  16. Kozak M (1989a) Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs. Mol Cell Biol 9:5134–5142. CrossRefPubMedPubMedCentralGoogle Scholar
  17. Kozak M (1989b) The scanning model for translation: an update. J Cell Biol 108:229–241CrossRefPubMedGoogle Scholar
  18. Lauressergues D, Couzigou J-M, San Clemente H, Martinez Y, Dunand C, Bécard G, Combier J-P (2015) Primary transcripts of microRNAs encode regulatory peptides. Nature 520:90–93. CrossRefPubMedGoogle Scholar
  19. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23:4051–4060. CrossRefPubMedPubMedCentralGoogle Scholar
  20. Li M, Doll J, Weckermann K, Oecking C, Berendzen KW, Schöffl F (2010) Detection of in vivo interactions between Arabidopsis class A-HSFs, using a novel BiFC fragment, and identification of novel class B-HSF interacting proteins. Eur J Cell Biol 89:126–132. CrossRefPubMedGoogle Scholar
  21. Lu J, Sivamani E, Azhakanandam K, Samadder P, Li X, Qu R (2008) Gene expression enhancement mediated by the 5′ UTR intron of the rice rubi3 gene varied remarkably among tissues in transgenic rice plants. Mol Genet Genomics 279:563–572. CrossRefPubMedGoogle Scholar
  22. Lu J, Gao F, Wei Z, Liu P, Zheng H, Yang L, Lin T, Yuan S. (2011) A 5′-proximal stem-loop structure of 5′untranslated region of porcine reproductive and respiratory syndrome virus genome is key for virus replication. Virol J 8(1):1–15. CrossRefGoogle Scholar
  23. Mayfield SP, Cohen A, Danon A, Yohn CB (1994) Translation of the psbA mRNA of Chlamydomonas reinhardtii requires a structured RNA element contained within the 5′ untranslated region. J Cell Biol 127:1537–1545CrossRefPubMedGoogle Scholar
  24. Mignone F, Gissi C, Liuni S, Pesole G (2002) Untranslated regions of mRNAs. Genome Biol 3(3):reviews0004-1CrossRefGoogle Scholar
  25. Nagashima S, Sasaki J, Taniguchi K (2005) The 5′-terminal region of the Aichi virus genome encodes cis-acting replication elements required for positive-and negative-strand RNA synthesis. J Virol 79:6918–6931. CrossRefPubMedPubMedCentralGoogle Scholar
  26. Pasternak AO, van den Born E, Spaan WJ, Snijder EJ (2003) The stability of the duplex between sense and antisense transcription-regulating sequences is a crucial factor in arterivirus subgenomic mRNA synthesis. J Virol 77:1175–1183. CrossRefPubMedPubMedCentralGoogle Scholar
  27. Pickering BM, Willis AE (2005) The implications of structured 5′ untranslated regions on translation and disease. Semin Cell Dev Biol 16(1):39–47. CrossRefPubMedGoogle Scholar
  28. Pina C, Pinto F, Feijó JA, Becker JD (2005) Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation. Plant Physiol 138:744–756. CrossRefPubMedPubMedCentralGoogle Scholar
  29. Satoh J, Kato K, Shinmyo A (2004) The 5′-untranslated region of the tobacco alcohol dehydrogenase gene functions as an effective translational enhancer in plant. J Biosci Bioeng 98:1–8. CrossRefPubMedGoogle Scholar
  30. Sugio T, Satoh J, Matsuura H, Shinmyo A, Kato K (2008) The 5′-untranslated region of the Oryza sativa alcohol dehydrogenase gene functions as a translational enhancer in monocotyledonous plant cells. J Biosci Bioeng 105:300–302. CrossRefPubMedGoogle Scholar
  31. Van Der Velden AW, Thomas AA (1999) The role of the 5′ untranslated region of an mRNA in translation regulation during development. Int J Biochem Cell Biol 31:87–106. CrossRefPubMedGoogle Scholar
  32. Vazquez F, Blevins T, Ailhas JM, Boller T, Meins F (2008) Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res 36:6429–6438. CrossRefPubMedPubMedCentralGoogle Scholar
  33. Wilkie GS, Dickson KS, Gray NK (2003) Regulation of mRNA translation by 5′-and 3′-UTR-binding factors. Trends Biochem Sci 28:182–188. CrossRefPubMedGoogle Scholar
  34. Yoo SD, Cho YH, Sheen J (2007) Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat Protoc 2:1565–1572. CrossRefPubMedGoogle Scholar

Copyright information

© Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków 2018

Authors and Affiliations

  1. 1.The Sichuan Provincial Key Laboratory for Human Disease Gene StudyHospital of the University of Electronic Science and Technology of China and Sichuan Provincial People’s HospitalChengduChina
  2. 2.School of Medical TechnologyChengdu University of Traditional Chinese MedicineChengduChina
  3. 3.National and Local Joint Engineering Laboratory for Energy Plant Bio-oil Production and Application, College of Life ScienceSichuan UniversityChengduChina
  4. 4.Biogas Institute of Ministry of AgricultureChengduChina

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