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Natural RNA circles function as efficient microRNA sponges

Abstract

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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Acknowledgements

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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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.

Corresponding authors

Correspondence to Thomas B. Hansen or Jørgen Kjems.

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The authors declare no competing financial interests.

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This file contains Supplementary Table 1, Supplementary Figures 1-10 and Supplementary References. (PDF 4182 kb)

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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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