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Computational Identification of MicroRNAs and Their Targets from Finger Millet (Eleusine coracana)

  • S. Usha
  • M. N. Jyothi
  • B. Suchithra
  • Rekha Dixit
  • D. V. Rai
  • R. Nagesh babuEmail author
Original Research Article

Abstract

MicroRNAs are endogenous small RNAs regulating intrinsic normal growth and development of plant. Discovering miRNAs, their targets and further inferring their functions had become routine process to comprehend the normal biological processes of miRNAs and their roles in plant development. In this study, we used homology-based analysis with available expressed sequence tag of finger millet (Eleusine coracana) to predict conserved miRNAs. Three potent miRNAs targeting 88 genes were identified. The newly identified miRNAs were found to be homologous with miR166 and miR1310. The targets recognized were transcription factors and enzymes, and GO analysis showed these miRNAs played varied roles in gene regulation. The identification of miRNAs and their targets is anticipated to hasten the pace of key epigenetic regulators in plant development.

Keywords

EST GO analysis MYB Transcription factors 

Notes

Acknowledgments

This work is supported by Department of Science and Technology (SR/FT/LS-10/2012), New Delhi, India.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Supplementary material

12539_2015_130_MOESM1_ESM.xlsx (10 kb)
Supplementary file 1 Precursor sequences of miRNAs in Finger millet (xlsx 9 kb)
12539_2015_130_MOESM2_ESM.xlsx (14 kb)
Supplementary file 2 GO terms for targets identified in Finger millet (xlsx 14 kb)

References

  1. 1.
    Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75(5):843–854CrossRefPubMedGoogle Scholar
  2. 2.
    Chen XM (2005) microRNA biogenesis and function in plants. FEBS Lett 579(26):5923–5931CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Carrington JC, Ambros V (2003) Role of micro RNAs in plant and animal development. Science 301(5631):336–338CrossRefPubMedGoogle Scholar
  4. 4.
    Sunkar R, Li YF, Jagadeeswaran G (2012) Functions of micro RNAs in plant stress responses. Trends Plant Sci 17(4):196–203CrossRefPubMedGoogle Scholar
  5. 5.
    Ambros V, Chen XM (2007) The regulation of genes and genomes by small RNAs. Development 134(9):1635–1641CrossRefPubMedGoogle Scholar
  6. 6.
    Akter A, Islam M, Mondal SI, Mahmud Z, Jewel NA, Ferdous S, Amin R, Rahman M (2013) Computational identification of miRNA and their targets from expressed sequence tags of Coffee (Coffea arabica). Saudi J Biol Sci 21(1):3–12CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Breakfield NW, Corcoran DL, Petricka JJ, Shen J, Sae-Seaw J, Rubio-Somoza I, Weigel D, Ohler U, Benfey PN (2012) High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. Genome Res 22(1):163–176CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Wang L, Liu H, Li D, Chen H (2011) Identification and characterization of maize microRNAs involved in the very early stage of seed germination. BMC Genom 12:154CrossRefGoogle Scholar
  9. 9.
    Wang C, Wei L, Guo M, Zou Q (2013) Computational approaches in detecting non-coding RNA. Curr Genomics 14(6):371–377CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Zou Q, Mao Y, Hu L, Wu Y, Ji Z (2014) miRClassify: an advanced web server for miRNA family classification and annotation. Comput Biol Med 45:157–160CrossRefPubMedGoogle Scholar
  11. 11.
    Chen H, Zhang Z (2013) Similarity-based methods for potential human microRNA-disease association prediction. BMC Med Genomics 6:12CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Zeng X, Zhang X, Zou Q (2015) Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks. Brief Bioinform. doi: 10.1093/bib/bbv033 Google Scholar
  13. 13.
    Zou Q, Li J, Hong Q, Lin Z, Wu Y, Shi H, Ju Y (2015) Prediction of microRNA-disease associations based on social network analysis methods. BioMed Res Int. doi: 10.1155/2015/810514 Google Scholar
  14. 14.
    Huang Y, Zou Q, Tang SM, Wang LG, Shen XJ (2010) Computational identification and characteristics of novel microRNAs from the silkworm (Bombyx mori L.). Mol Biol Rep 37(7):3171–3176CrossRefPubMedGoogle Scholar
  15. 15.
    Hong Xi, Zhao Ling Ping, Zou Quan, Wang Zhan Bin (2014) Identification of microRNA genes and their mRNA targets in Festuca arundinacea. Appl Biochem Biotechnol 172(8):3875–3887CrossRefGoogle Scholar
  16. 16.
    Huang Y, Zou Q, Wang ZB (2014) Computational identification of miRNA genes and their targets in mulberry. Russ J Plant Physiol 61(4):537–542CrossRefGoogle Scholar
  17. 17.
    Liu Y, Chang W, Han Y, Zou Q, Guo M, Li WB (2011) In silico detection of novel microRNAs genes in soybean genome. Agric Sci China 10(9):1336–1345CrossRefGoogle Scholar
  18. 18.
    Huang Y, Zou Q, Sun XH, Zhao LP (2014) Computational identification of microRNAs and their targets in perennial Ryegrass (Lolium perenne). Appl Biochem Biotechnol 173(4):1011–1022CrossRefPubMedGoogle Scholar
  19. 19.
    Ding J, Li D, Ohler U, Guan J, Zhou S (2012) Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach. BMC Genom 13:S3CrossRefGoogle Scholar
  20. 20.
    Sun F, Guo G, Guo W, Peng H, Ni Z, Sun Q, Yao Y (2014) Whole-genome discovery of miRNAs and their targets in wheat (Triticum aestivum L.). BMC Plant Biol 14:142CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Chen R, Hu Z, Zhang H (2009) Identification of microRNAs in wild soybean (Glycine soja). J Integr Plant Biol 51(12):1071–1079CrossRefPubMedGoogle Scholar
  22. 22.
    Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C (2008) A diverse set of microRNAs and microRNA like small RNAs in developing rice grains. Genome Res 18(9):456–1465CrossRefGoogle Scholar
  23. 23.
    Frazier TP, Xie F, Freistaedter A, Burklew CE, Zhang B (2010) Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta 232(6):1289–1308CrossRefPubMedGoogle Scholar
  24. 24.
    Ambros V, Bartel B, Bartel DP (2003) A uniform system for microRNA annotation. RNA 9(3):277–279CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Chi X, Yang Q, Chen X, Wang J et al (2011) Identification and characterization of microRNAs from peanut (Arachis hypogaea L.) by high throughput sequencing. PLoS ONE 6(11):e27530CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Xu L, Wang Y, Xu Y, Wang L, Zhai L et al (2013) Identification and characterization of novel and conserved microRNAs in radish (Raphanus sativus L.) using high-throughput sequencing. Plant Sci 201–202:108–114CrossRefPubMedGoogle Scholar
  27. 27.
    Bonnet E, Wuyts J, Rouze P, Peer YV (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20(17):2911–2917CrossRefPubMedGoogle Scholar
  28. 28.
    Han Y, Luan F, Zhu H, Shao Y, Chen A, Lu C, Luo Y, Zhu B (2009) Computational identification of microRNAs and their targets in wheat (Triticum aestivum L.). Sci China Ser C Life Sci 52(11):1091–1100CrossRefGoogle Scholar
  29. 29.
    Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39(Web Server issue):W155–W159CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Giacomelli JI, Weigel D, Chan RL, Manavella PA (2012) Role of recently evolved miRNA regulation of sunflower HaWRKY6 in response to temperature damage. New Phytol 195(4):766–773CrossRefPubMedGoogle Scholar
  31. 31.
    Alonso-Peral MM, Li J, Li Y, Allen RS, Schnippenkoetter W, Ohms S, White RG, Millar AA (2010) The microRNA159-regulated GAMYB-like genes inhibit growth and promote programmed cell death in Arabidopsis. Plant Physiol 154(2):757–771CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Cecchetti V, Altamura MM, Falasca G, Costantino P, Cardarelli M (2008) Auxin regulates Arabidopsis anther dehiscence, pollen maturation, and filament elongation. Plant Cell 20(7):1760–1774CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Dharmasiri N, Dharmasiri S, Weijers D, Lechner E, Yamada M, Hobbie L et al (2005) Plant development is regulated by a family of auxin receptor F box proteins. Dev Cell 9(1):109–119CrossRefPubMedGoogle Scholar
  34. 34.
    Thelander M, Fredriksson D, Schouten J, Hoge JH, Ronne H (2002) Cloning by pathway activation in yeast: identification of an Arabidopsis thaliana F-box protein that can turn on glucose repression. Plant Mol Biol 49(1):69–79CrossRefPubMedGoogle Scholar
  35. 35.
    Parry G, Ward S, Cernac A, Dharmasiri S, Estelle M (2006) The Arabidopsis SUPPRESSOR OF AUXIN RESISTANCE Proteins are nucleoporins with an important role in hormone signaling and development. The Plant 18(7):1590–1603Google Scholar
  36. 36.
    Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9(9):868–877CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406–3415CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Wei L, Liao M, Gao Y, Ji R, He Z, Zou Q (2013) Improved and promising identification of human microRNAs by incorporating a high-quality negative set. IEEE/ACM Trans Comput Biol Bioinf 11(1):192–201CrossRefGoogle Scholar
  39. 39.
    Ye J, Fang L et al (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34(Web service issue):W293–W297CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • S. Usha
    • 1
    • 2
  • M. N. Jyothi
    • 1
    • 2
  • B. Suchithra
    • 1
  • Rekha Dixit
    • 2
  • D. V. Rai
    • 2
  • R. Nagesh babu
    • 1
    Email author
  1. 1.Maharani’s Science College for WomenBangaloreIndia
  2. 2.Faculty of Biological EngineeringShobhit UniversityMeerutIndia

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