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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Bartel, D. P. MicroRNAs: target recognition and regulatory functions. Cell 136, 215–233 (2009)
Franco-Zorrilla, J. M. et al. Target mimicry provides a new mechanism for regulation of microRNA activity. Nature Genet. 39, 1033–1037 (2007)
Poliseno, L. et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465, 1033–1038 (2010)
Cesana, M. et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147, 358–369 (2011)
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)
Tay, Y. et al. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 147, 344–357 (2011)
Sumazin, P. et al. An extensive microRNA-mediated network of RNA–RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147, 370–381 (2011)
Hansen, T. B. et al. miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J. 30, 4414–4422 (2011)
Capel, B. et al. Circular transcripts of the testis-determining gene Sry in adult mouse testis. Cell 73, 1019–1030 (1993)
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)
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)
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)
Hutvágner, G. & Zamore, P. D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056–2060 (2002)
Chi, S. W., Zang, J. B., Mele, A. & Darnell, R. B. Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps. Nature 460, 479–486 (2009)
Bak, M. et al. MicroRNA expression in the adult mouse central nervous system. RNA 14, 432–444 (2008)
Pasman, Z., Been, M. D. & Garcia-Blanco, M. A. Exon circularization in mammalian nuclear extracts. RNA 2, 603–610 (1996)
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)
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)
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)
Junn, E. et al. Repression of α-synuclein expression and toxicity by microRNA-7. Proc. Natl Acad. Sci. USA 106, 13052–13057 (2009)
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)
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)
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)
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)
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)
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)
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)
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)
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.
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). https://doi.org/10.1038/nature11993
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