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Natural RNA circles function as efficient microRNA sponges


MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs1. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called competing endogenous RNA in humans and target mimicry in plants2,3,4,5,6,7. We previously identified a highly expressed circular RNA (circRNA) in human and mouse brain8. Here we show that this circRNA acts as a miR-7 sponge; we term this circular transcript ciRS-7 (circular RNA sponge for miR-7). ciRS-7 contains more than 70 selectively conserved miRNA target sites, and it is highly and widely associated with Argonaute (AGO) proteins in a miR-7-dependent manner. Although the circRNA is completely resistant to miRNA-mediated target destabilization, it strongly suppresses miR-7 activity, resulting in increased levels of miR-7 targets. In the mouse brain, we observe overlapping co-expression of ciRS-7 and miR-7, particularly in neocortical and hippocampal neurons, suggesting a high degree of endogenous interaction. We further show that the testis-specific circRNA, sex-determining region Y (Sry)9, serves as a miR-138 sponge, suggesting that miRNA sponge effects achieved by circRNA formation are a general phenomenon. This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA.

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Figure 1: Structure, conservation and heterologous expression of ciRS-7.
Figure 2: Interaction between ciRS-7 and miR-7.
Figure 3: ciRS-7 acts as a sponge for miR-7 activity.
Figure 4: Circular Sry RNA interacts with miR-138.

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  1. Bartel, D. P. MicroRNAs: target recognition and regulatory functions. Cell 136, 215–233 (2009)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Franco-Zorrilla, J. M. et al. Target mimicry provides a new mechanism for regulation of microRNA activity. Nature Genet. 39, 1033–1037 (2007)

    Article  CAS  PubMed  Google Scholar 

  3. Poliseno, L. et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465, 1033–1038 (2010)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  4. Cesana, M. et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147, 358–369 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Karreth, F. A. et al. In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell 147, 382–395 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Tay, Y. et al. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 147, 344–357 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Sumazin, P. et al. An extensive microRNA-mediated network of RNA–RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147, 370–381 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Hansen, T. B. et al. miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J. 30, 4414–4422 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Capel, B. et al. Circular transcripts of the testis-determining gene Sry in adult mouse testis. Cell 73, 1019–1030 (1993)

    Article  CAS  PubMed  Google Scholar 

  10. Ebert, M. S., Neilson, J. R. & Sharp, P. A. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nature Methods 4, 721–726 (2007)

    Article  CAS  PubMed  Google Scholar 

  11. Bailey, T. L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28–36 (1994)

    CAS  PubMed  Google Scholar 

  12. Elbashir, S. M., Martinez, J., Patkaniowska, A., Lendeckel, W. & Tuschl, T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20, 6877–6888 (2001)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Hutvágner, G. & Zamore, P. D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056–2060 (2002)

    Article  ADS  PubMed  Google Scholar 

  14. Chi, S. W., Zang, J. B., Mele, A. & Darnell, R. B. Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps. Nature 460, 479–486 (2009)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  15. Bak, M. et al. MicroRNA expression in the adult mouse central nervous system. RNA 14, 432–444 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Pasman, Z., Been, M. D. & Garcia-Blanco, M. A. Exon circularization in mammalian nuclear extracts. RNA 2, 603–610 (1996)

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Dubin, R. A., Kazmi, M. A. & Ostrer, H. Inverted repeats are necessary for circularization of the mouse testis Sry transcript. Gene 167, 245–248 (1995)

    Article  CAS  PubMed  Google Scholar 

  18. Iioka, H., Loiselle, D., Haystead, T. A. & Macara, I. G. Efficient detection of RNA-protein interactions using tethered RNAs. Nucleic Acids Res. 39, e53 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Liu, J., Valencia-Sanchez, M. A., Hannon, G. J. & Parker, R. MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nature Cell Biol. 7, 719–723 (2005)

    Article  CAS  PubMed  Google Scholar 

  20. Junn, E. et al. Repression of α-synuclein expression and toxicity by microRNA-7. Proc. Natl Acad. Sci. USA 106, 13052–13057 (2009)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kefas, B. et al. microRNA-7 inhibits the epidermal growth factor receptor and the Akt pathway and is down-regulated in glioblastoma. Cancer Res. 68, 3566–3572 (2008)

    Article  CAS  PubMed  Google Scholar 

  22. Jiang, L. et al. MicroRNA-7 targets IGF1R (insulin-like growth factor 1 receptor) in tongue squamous cell carcinoma cells. Biochem. J. 432, 199–205 (2010)

    Article  CAS  PubMed  Google Scholar 

  23. Salzman, J., Gawad, C., Wang, P. L., Lacayo, N. & Brown, P. O. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE 7, e30733 (2012)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  24. Reddy, S. D., Ohshiro, K., Rayala, S. K. & Kumar, R. MicroRNA-7, a homeobox D10 target, inhibits p21-activated kinase 1 and regulates its functions. Cancer Res. 68, 8195–8200 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Hendrickson, D. G., Hogan, D. J., Herschlag, D., Ferrell, J. E. & Brown, P. O. Systematic identification of mRNAs recruited to Argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS ONE 3, e2126 (2008)

    Article  ADS  PubMed  PubMed Central  Google Scholar 

  26. Lykke-Andersen, J. & Wagner, E. Recruitment and activation of mRNA decay enzymes by two ARE-mediated decay activation domains in the proteins TTP and BRF-1. Genes Dev. 19, 351–361 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Clausen, B. H. et al. Interleukin-1β and tumor necrosis factor-α are expressed by different subsets of microglia and macrophages after ischemic stroke in mice. J. Neuroinflammation 5, 46 (2008)

    Article  PubMed  PubMed Central  Google Scholar 

  28. Clausen, B. H., Lambertsen, K. L. & Finsen, B. Glyceraldehyde-3-phosphate dehydrogenase versus toluidine blue as a marker for infarct volume estimation following permanent middle cerebral artery occlusion in mice. Exp. Brain Res. 175, 60–67 (2006)

    Article  CAS  PubMed  Google Scholar 

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We thank C. Bus and R. Rosendahl for technical assistance and R. M. Zadegan for art work. We also thank the G. Hannon laboratory for providing us with the Myc-tagged AGO2 expression vector, J. Lykke-Andersen for the DCP1A antibody, and K. L. Lambertsen and C. U. von Linstow for their assistance with confocal microscopy. This work was supported by the SIROCCO EU consortium, the Lundbeck Foundation, and the Danish Council for Independent Research - Natural Sciences. T.B.H. and B.H.C. were supported by the Lundbeck Foundation.

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Authors and Affiliations



T.B.H. conceived the project, designed the experiments and drafted the manuscript. T.B.H., T.I.J. and C.K.D. performed the experiments. J.B.B. assisted experimentally and intellectually. B.H.C. performed the brain in situ hybridizations. B.F., C.K.D. and J.K. supervised the project and revised the manuscript.

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Correspondence to Thomas B. Hansen or Jørgen Kjems.

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The authors declare no competing financial interests.

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Hansen, T., Jensen, T., Clausen, B. et al. Natural RNA circles function as efficient microRNA sponges. Nature 495, 384–388 (2013).

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