Skip to main content
SpringerLink
Log in

Characterization of microRNAs from sheep (Ovis aries) using computational and experimental analyses

  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Ovis aries is one of the most important agricultural livestock for meat production, and also is an ideal model organism for biological and comparative genomics studies. Many miRNAs have been reported for their important roles in developmental processes in various animals, but there is limited information about O. aries miRNAs. In this study, combining a computational method based on expressed sequence tag (EST) analysis with experimental identification based on small RNA cDNA library, we identified 31 miRNAs belong to 24 families in sheep, 2 of which were novel miRNAs which had never been previously identified in any species. Especially, we cloned 12 miRNAs from the sheep skeletal muscle, which were good candidate miRNAs to be studied about the miRNA-dependant regulated process of muscle development, and we identified four pairs of miRNA/miRNA* and one pair of miRNA-3p/miRNA-5p from sheep EST sequences. Expression analysis indicated that some miRNAs were expressed in a specific tissue, and the pair of miRNA-3p/miRNA-5p and one pair of miRNA/miRNA* had a similar relative expression pattern in some tissues, respectively. Further, we predicted 120 potential target genes of 31 oar-miRNAs on the 3′UTR of O. aries genes. Gene ontology analysis showed that most of these genes took part in the cellular process and metabolic process. Our results enriched the O. aries miRNA database and provided useful information for investigating biological functions of miRNAs and miRNA* in sheep.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  PubMed  CAS  Google Scholar 

  2. Pillai RS, Bhattacharyya SN, Filipowicz W (2007) Repression of protein synthesis by miRNAs: how many mechanisms? Trends Cell Biol 17:118–126

    Article  PubMed  CAS  Google Scholar 

  3. Place RF, Li LC, Pookot D, Noonan EJ, Dahiya R (2008) MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci USA 105:1608–1613

    Article  PubMed  CAS  Google Scholar 

  4. Vasudevan S, Tong Y, Steitz JA (2007) Switching from repression to activation: microRNAs can up-regulate translation. Science 318:1931–1934

    Article  PubMed  CAS  Google Scholar 

  5. Johnston RJ, Hobert O (2003) A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426:845–849

    Article  PubMed  CAS  Google Scholar 

  6. Chang S, Johnston RJ Jr, Frokjaer-Jensen C, Lockery S, Hobert O (2004) MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature 430:785–789

    Article  PubMed  CAS  Google Scholar 

  7. Hatfield SD, Shcherbata HR, Fischer KA, Nakahara K, Carthew RW, Ruohola-Baker H (2005) Stem cell division is regulated by the microRNA pathway. Nature 435:974–978

    Article  PubMed  CAS  Google Scholar 

  8. Poy MN, Eliasson L, Krutzfeldt J, Kuwajima S, Ma X, Macdonald PE, Pfeffer S, Tuschl T, Rajewsky N, Rorsman P, Stoffel M (2004) A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432:226–230

    Article  PubMed  CAS  Google Scholar 

  9. Xu P, Vernooy SY, Guo M, Hay BA (2003) The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr Biol 13:790–795

    Article  PubMed  CAS  Google Scholar 

  10. Lee YS, Dutta A (2007) The tumor suppressor microRNA let-7 represses the HMGA2 oncogene. Genes Dev 21:1025–1030

    Article  PubMed  CAS  Google Scholar 

  11. Tavazoie SF, Alarcon C, Oskarsson T, Padua D, Wang Q, Bos PD, Gerald WL, Massague J (2008) Endogenous human microRNAs that suppress breast cancer metastasis. Nature 451:147–152

    Article  PubMed  CAS  Google Scholar 

  12. Calin GA, Ferracin M, Cimmino A, Di Leva G, Shimizu M, Wojcik SE, Iorio MV, Visone R, Sever NI, Fabbri M, Iuliano R, Palumbo T, Pichiorri F, Roldo C, Garzon R, Sevignani C, Rassenti L, Alder H, Volinia S, Liu CG, Kipps TJ, Negrini M, Croce CM (2005) A microRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 353:1793–1801

    Article  PubMed  CAS  Google Scholar 

  13. Liu T, Tang H, Lang Y, Liu M, Li X (2009) MicroRNA-27a functions as an oncogene in gastric adenocarcinoma by targeting prohibition. Cancer Lett 273:233–242

    Article  PubMed  CAS  Google Scholar 

  14. Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T (2003) New microRNAs from mouse and human. RNA 9:175–179

    Article  PubMed  CAS  Google Scholar 

  15. Fu H, Tie Y, Xu C, Zhang Z, Zhu J, Shi Y, Jiang H, Sun Z, Zheng X (2005) Identification of human fetal liver miRNAs by a novel method. FEBS Lett 579:3849–3854

    Article  PubMed  CAS  Google Scholar 

  16. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115:787–798

    Article  PubMed  CAS  Google Scholar 

  17. Chang YM, Juan HF, Lee TY, Chang YY, Yeh YM, Li WH, Shih AC (2008) Prediction of human miRNAs using tissue-selective motifs in 3′ UTRs. Proc Natl Acad Sci USA 105:17061–17066

    Article  PubMed  CAS  Google Scholar 

  18. Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP (2003) Vertebrate microRNA genes. Science 299:1540

    Article  PubMed  CAS  Google Scholar 

  19. Huang TH, Zhu MJ, Li XY, Zhao SH (2008) Discovery of porcine microRNAs and profiling from skeletal muscle tissues during development. PLoS ONE 3:e3225

    Article  PubMed  Google Scholar 

  20. Alexander Stark PK, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M (2008) Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res 17:1865–1879

    Article  Google Scholar 

  21. Singh J, Nagaraju J (2008) In silico prediction and characterization of microRNAs from red flour beetle (Tribolium castaneum). Insect Mol Biol 17:427–436

    Article  PubMed  CAS  Google Scholar 

  22. Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V (2005) Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res 15:78–91

    Article  PubMed  CAS  Google Scholar 

  23. Pan XP, Zhang BH, Wang QL, Cobb GP, Anderson TA (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Res 15:336–360

    Google Scholar 

  24. Weibo Jin NL, Zhang B, Wu F, Li W, Guo A, Deng Z (2008) Identification and verification of microRNA in wheat (Triticum aestivum). J Plant Res 121:351–355

    Article  PubMed  Google Scholar 

  25. Griffiths-Jones S (2004) The microRNA registry. Nucleic Acids Res 32:D109–D111

    Article  PubMed  CAS  Google Scholar 

  26. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34:D140–D144

    Article  PubMed  CAS  Google Scholar 

  27. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158

    Article  PubMed  CAS  Google Scholar 

  28. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, Bibe B, Bouix J, Caiment F, Elsen JM, Eychenne F, Larzul C, Laville E, Meish F, Milenkovic D, Tobin J, Charlier C, Georges M (2006) A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet 38:813–818

    Article  PubMed  CAS  Google Scholar 

  29. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  30. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415

    Article  PubMed  CAS  Google Scholar 

  31. Mathews DH, Sabina J, Zuker M, Turner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288:911–940

    Article  PubMed  CAS  Google Scholar 

  32. Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858–862

    Article  PubMed  CAS  Google Scholar 

  33. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33:e179

    Article  PubMed  Google Scholar 

  34. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20

    Article  PubMed  CAS  Google Scholar 

  35. Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10:1507–1517

    Article  PubMed  CAS  Google Scholar 

  36. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T (2003) A uniform system for microRNA annotation. RNA 9:277–279

    Article  PubMed  CAS  Google Scholar 

  37. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294:853–858

    Article  PubMed  CAS  Google Scholar 

  38. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol 12:735–739

    Article  PubMed  CAS  Google Scholar 

  39. Jin W, Grant JR, Stothard P, Moore SS, Guan LL (2009) Characterization of bovine miRNAs by sequencing and bioinformatics analysis. BMC Mol Biol 10:90

    Article  PubMed  Google Scholar 

  40. Kim J, Cho IS, Hong JS, Choi YK, Kim H, Lee YS (2008) Identification and characterization of new microRNAs from pig. Mamm Genome 19:570–580

    Article  PubMed  CAS  Google Scholar 

  41. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127:1193–1207

    Article  PubMed  CAS  Google Scholar 

  42. Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC (2007) Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res 17:1850–1864

    Article  PubMed  CAS  Google Scholar 

  43. Weber MJ (2005) New human and mouse microRNA genes found by homology search. FEBS J 272:59–73

    Article  PubMed  CAS  Google Scholar 

  44. Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H (2005) Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 33:2697–2706

    Article  PubMed  CAS  Google Scholar 

  45. He PA, Nie Z, Chen J, Chen J, Lv Z, Sheng Q, Zhou S, Gao X, Kong L, Wu X, Jin Y, Zhang Y (2008) Identification and characteristics of microRNAs from Bombyx mori. BMC Genomics 9:248

    Article  PubMed  Google Scholar 

  46. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  PubMed  CAS  Google Scholar 

  47. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434:338–345

    Article  PubMed  CAS  Google Scholar 

  48. Goll DE, Thompson VF, Li H, Wei W, Cong J (2003) The calpain system. Physiol Rev 83:731–801

    PubMed  CAS  Google Scholar 

  49. Wendt A, Thompson VF, Goll DE (2004) Interaction of calpastatin with calpain: a review. Biol Chem 385:465–472

    Article  PubMed  CAS  Google Scholar 

  50. Perry RL, Rudnick MA (2000) Molecular mechanisms regulating myogenic determination and differentiation. Front Biosci 5:D750–D767

    Article  PubMed  CAS  Google Scholar 

  51. Zhang H, Stavnezer E (2009) Ski regulates muscle terminal differentiation by transcriptional activation of Myog in a complex with Six1 and Eya3. J Biol Chem 284:2867–2879

    Article  PubMed  CAS  Google Scholar 

  52. Wang X, Zhang J, Li F, Gu J, He T, Zhang X, Li Y (2005) MicroRNA identification based on sequence and structure alignment. Bioinformatics 21:3610–3614

    Article  PubMed  CAS  Google Scholar 

  53. Anton I, Zsolnai A, Komlosi I, Kiraly A, Fesus L (2006) Effect of MYOG genotypes on growth rate and production traits in Hungarian large white pigs. Acta Vet Hung 54:393–397

    Article  PubMed  CAS  Google Scholar 

  54. Van Laere AS, Nguyen M, Braunschweig M, Nezer C, Collette C, Moreau L, Archibald AL, Haley CS, Buys N, Tally M, Andersson G, Georges M, Andersson L (2003) A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425:832–836

    Article  PubMed  Google Scholar 

  55. Coleman ME, DeMayo F, Yin KC, Lee HM, Geske R, Montgomery C, Schwartz RJ (1995) Myogenic vector expression of insulin-like growth factor I stimulates muscle cell differentiation and myofiber hypertrophy in transgenic mice. J Biol Chem 270:12109–12116

    Article  PubMed  CAS  Google Scholar 

  56. Chen JF, Mandel EM, Thomson JM, Wu Q, Callis TE, Hammond SM, Conlon FL, Wang DZ (2006) The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 38:228–233

    Article  PubMed  CAS  Google Scholar 

  57. Naguibneva I, Ameyar-Zazoua M, Polesskaya A, Ait-Si-Ali S, Groisman R, Souidi M, Cuvellier S, Harel-Bellan A (2006) The microRNA miR-181 targets the homeobox protein Hox-A11 during mammalian myoblast differentiation. Nat Cell Biol 8:278–284

    Article  PubMed  CAS  Google Scholar 

  58. Sunkar R, Jagadeeswaran G (2008) In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol 8:37

    Article  PubMed  Google Scholar 

  59. Kim HK, Lee YS, Sivaprasad U, Malhotra A, Dutta A (2006) Muscle-specific microRNA miR-206 promotes muscle differentiation. J Cell Biol 174:677–687

    Article  PubMed  CAS  Google Scholar 

  60. Lim LP, Lua NC, Weinstein EG et al (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17(8):991–1008

    Article  PubMed  CAS  Google Scholar 

  61. Qiu CX, Xie FL, Zhu YY, Guo K, Huang SQ, Nie L, Yang ZM (2007) Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags. Gene 395:49–61

    Article  PubMed  CAS  Google Scholar 

  62. Yin Z, Li C, Han X, Shen F (2008) Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene 414:60–66

    Article  PubMed  CAS  Google Scholar 

  63. Zhang B, Wang Q, Wang K, Pan X, Liu F, Guo T, Cobb GP, Anderson TA (2007) Identification of cotton microRNAs and their targets. Gene 397:26–37

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by national High Technology Research and Development Program (863 Program) (No. 2006AA10Z199) and New Special Sheep Varieties with Top Quality Selection Program (No. 2006BAD01A11). We would like to thank Yanchun Yan, Hunter Linda, Zhengkui Zhou, Kejia Wu, Tinghua Huang, Shengsong Xie for language help and technical assistance.

Author information

Authors and Affiliations

  1. National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, People’s Republic of China

    Xihui Sheng, Caihong Wei, Tao Liu, Li Zhang & Lixin Du

  2. College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA

    Xihui Sheng

  3. The Institute of Animal Husbandry and Veterinary Science, ZheJiang Academy Of Agricultural Sciences, Shiqiao Rd., Hangzhou, Zhejiang, 310021, People’s Republic of China

    Xuemei Song

  4. Reproductive Medical Center, The Second Hospital Affiliated to Shandong University of Traditional Chinese Medicine, Jinan, 250001, People’s Republic of China

    Yan Yu

  5. Division of Applied Life Science, Graduate School of Gyeongsang National University, Jinju, 660-701, Korea

    Lili Niu

  6. Department of Laboratory Animal Sciences, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, People’s Republic of China

    Shangang Li

  7. Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People’s Republic of China

    Hongbin Li

Authors
  1. Xihui Sheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xuemei Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yan Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lili Niu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shangang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hongbin Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Caihong Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Tao Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Li Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Lixin Du
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Lixin Du.

Electronic supplementary material

Below is the link to the electronic supplementary material.

(EPS 3904 kb)

(DOC 26 kb)

(DOC 238 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sheng, X., Song, X., Yu, Y. et al. Characterization of microRNAs from sheep (Ovis aries) using computational and experimental analyses. Mol Biol Rep 38, 3161–3171 (2011). https://doi.org/10.1007/s11033-010-9987-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-010-9987-3

Keywords

Search

Navigation