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A genome-wide screen for non-template nucleotides and isomiR repertoires in miRNAs indicates dynamic and versatile microRNAome

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Abstract

miRNA variants (termed isomiRs) have been reported as potential functional molecules that may affect miRNA stability or target selection. The aims of the present study were to comprehensively survey and characterize non-template nucleotides (NTNs) and isomiR repertoires in miRNAs. Over 50 % of the NTNs were located in the 3′ ends (also termed 3′ additions), followed by the 5′ ends and adjacent positions to 5′ and 3′ ends. The similar distributions of NTNs and isomiR repertoires might be detected between homologous or clustered miRNAs. miRNA might be stably expressed based on the typical analysis, but its isomiRs might be strongly up- or down-regulated. IsomiRs with novel seed sequences were mainly derived from “seed shifting” events in 5′ isomiRs, NTNs in 5′ ends or in seed sequences. IsomiRs from a miRNA locus or homologous miRNA loci maybe have the same seed sequences, but they would have various enrichment levels and 3′ ends. Interestingly, isomiR species with novel seed sequences via NTNs in the seed region were always stably expressed. These novel seed sequences could lead to novel functional roles through driving the potential novel target mRNAs. Integrated predicted target mRNAs and further microarray validation showed that these isomiRs have versatile biological roles. Collectively, multiple isomiR products and miRNA maturation processes provide opportunities to perform versatile roles in the regulatory network, which further enriches and complicates the regulation of biological processes.

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References

  1. Carthew RW, Sontheimer EJ (2009) Origins and Mechanisms of miRNAs and siRNAs. Cell 136:642–655

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  2. Guo H, Ingolia NT, Weissman JS, Bartel DP (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466:835–840

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  3. Huntzinger E, Izaurralde E (2011) Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet 12:99–110

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  5. Lai EC (2002) Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 30:363–364

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  7. Betel D, Wilson M, Gabow A, Marks DS, Sander C (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res 36:D149–D153

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19:92–105

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L et al (2005) Combinatorial microRNA target predictions. Nat Genet 37:495–500

    Article  CAS  PubMed  Google Scholar 

  10. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N et al (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129:1401–1414

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V et al (2008) Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res 18:571–584

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  12. Guo L, Yang Q, Lu J, Li H, Ge Q et al (2011) A comprehensive survey of miRNA repertoire and 3′ addition events in the placentas of patients with pre-eclampsia from high-throughput sequencing. PLoS One 6:e21072

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Neilsen CT, Goodall GJ, Bracken CP (2012) IsomiRs: the overlooked repertoire in the dynamic microRNAome. Trends Genet 28:544–549

    Article  CAS  PubMed  Google Scholar 

  14. Lee LW, Zhang S, Etheridge A, Ma L, Martin D et al (2010) Complexity of the microRNA repertoire revealed by next generation sequencing. RNA 16:2170–2180. doi:10.1261/rna.2225110

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. Burroughs AM, Ando Y, de Hoon MJL, Tomaru Y, Nishibu T et al (2010) A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness. Genome Res 20:1398–1410

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. Guo L, Li H, Lu J, Yang Q, Ge Q et al (2012) Tracking miRNA precursor metabolic products and processing sites through completely analyzing high-throughput sequencing data. Mol Biol Rep 39:2031–2038

    Article  CAS  PubMed  Google Scholar 

  17. Ebhardt HA, Tsang HH, Dai DC, Liu YF, Bostan B et al (2009) Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res 37:2461–2470

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Fernandez-Valverde SL, Taft RJ, Mattick JS (2010) Dynamic isomiR regulation in Drosophila development. RNA 16:1881–1888

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39:D152–D157

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. John B, Enright AJ, Aravin A, Tuschl T, Sander C et al (2004) Human MicroRNA targets. PLoS Biol 2:e363

    Article  PubMed Central  PubMed  Google Scholar 

  21. Lu SF, Sun YH, Chiang VL (2009) Adenylation of plant miRNAs. Nucleic Acids Res 37:1878–1885

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  22. Reid JG, Nagaraja AK, Lynn FC, Drabek RB, Muzny DM et al (2008) Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5′-seed/cleavage/anchor regions and stabilize predicted mmu-let-7a: mRNA duplexes. Genome Res 18:1571–1581

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. Lee Y, Jeon K, Lee JT, Kim S, Kim VN (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 21:4663–4670

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  24. Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B et al (2002) miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 16:720–728

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Lai EC, Tomancak P, Williams RW, Rubin GM (2003) Computational identification of Drosophila microRNA genes. Genome Biol 4:R42

    Article  PubMed Central  PubMed  Google Scholar 

  27. Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D et al (2003) The small RNA profile during Drosophila melanogaster development. Dev Cell 5:337–350

    Article  CAS  PubMed  Google Scholar 

  28. Guo L, Lu Z (2010) Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data. Comput Biol Chem 34:165–171

    Article  CAS  PubMed  Google Scholar 

  29. Guo L, Zhao Y, Zhang H, Yang S, Chen F (2013) Close association between paralogous multiple isomiRs and paralogous/orthologues miRNA sequences implicates dominant sequence selection across various animal species. Gene 527:624–629

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Acknowledgments

We thank Dr. Tao Chen for the statistical analysis. This work was supported by the National Natural Science Foundation of China (Nos. 61301251, 81072389 and 81373102), the Research Fund for the Doctoral Program of Higher Education of China (Nos. 211323411002 and 20133234120009), the China Postdoctoral Science Foundation funded project (No. 2012M521100), the key Grant of the Natural Science Foundation of the Jiangsu Higher Education Institutions of China (No. 10KJA33034), the National Natural Science Foundation of Jiangsu (No. BK20130885), the Natural Science Foundation of the Jiangsu Higher Education Institutions (Nos. 12KJB310003 and 13KJB330003), the Jiangsu Planned Projects for Postdoctoral Research Funds (No. 1201022B), the Science and Technology Development Fund Key Project of Nanjing Medical University (No. 2012NJMU001), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

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Authors and Affiliations

  1. Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China

    Li Guo, Yang Zhao, Sheng Yang, Hui Zhang & Feng Chen

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  1. Li Guo
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  2. Yang Zhao
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  3. Sheng Yang
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  4. Hui Zhang
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  5. Feng Chen
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Corresponding author

Correspondence to Feng Chen.

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Fig. S1

The same seed sequences between the different isomiRs from homologous miRNAs (a) or the same miRNA locus (b). Although these isomiRs have various sequences, even involved in non-template nucleotides, they may have the same seed sequences

Supplementary material 2 (DOCX 13 kb)

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Guo, L., Zhao, Y., Yang, S. et al. A genome-wide screen for non-template nucleotides and isomiR repertoires in miRNAs indicates dynamic and versatile microRNAome. Mol Biol Rep 41, 6649–6658 (2014). https://doi.org/10.1007/s11033-014-3548-0

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  • DOI: https://doi.org/10.1007/s11033-014-3548-0

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