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A distinct class of small RNAs arises from pre-miRNA–proximal regions in a simple chordate

Nature Structural & Molecular Biology volume 16, pages 183–189 (2009)Cite this article

Abstract

MicroRNAs (miRNAs) have been implicated in various cellular processes. They are thought to function primarily as inhibitors of gene activity by attenuating translation or promoting mRNA degradation. A typical miRNA gene produces a predominant ∼21-nucleotide (nt) RNA (the miRNA) along with a less abundant miRNA* product. We sought to identify miRNAs from the simple chordate Ciona intestinalis through comprehensive sequencing of small RNA libraries created from different developmental stages. Unexpectedly, half of the identified miRNA loci encode up to four distinct, stable small RNAs. The additional RNAs, miRNA-offset RNAs (moRs), are generated from sequences immediately adjacent to the predicted ∼60-nt pre-miRNA. moRs seem to be produced by RNAse III–like processing, are ∼20 nt long and, like miRNAs, are observed at specific developmental stages. We present evidence suggesting that the biogenesis of moRs results from an intrinsic property of the miRNA processing machinery in C. intestinalis.

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Figure 1: Developmental expression of small RNAs encoded by the C. intestinalis miR-219 locus.
Figure 2: Coincident expression of 5′ and 3′ moR sequences from the C. intestinalis miR-124 locus.
Figure 3: Direct detection of the 5′-moR-133 species.
Figure 4: Ectopic expression of Drosophila pri-miRNAs can induce moR production in C. intestinalis embryos.
Figure 5: A speculative model for the biogenesis of moRs.

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Acknowledgements

We thank L. Tonkin of the Vincent J. Coates Genomics Sequencing Laboratory for assistance with high-throughput sequencing and general expertise, H. Melichar for critical reading of the manuscript and members of the Levine laboratory for discussions. B.H. is supported by an American Cancer Society Postdoctoral Fellowship. This work was funded by a grant from the US National Institutes of Health (34431) to M.L.,

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Author notes

  1. Weiyang Shi and David Hendrix: These authors contributed equally to the work.

Authors and Affiliations

  1. Department of Molecular Cell Biology, Division of Genetics, Genomics, and Development, Center for Integrative Genomics, University of California, Berkeley, 94720-3200, California, USA

    Weiyang Shi, David Hendrix, Mike Levine & Benjamin Haley

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  1. Weiyang Shi
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  2. David Hendrix
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Contributions

W.S. and B.H. performed all experiments on C. intestinalis and D. melanogaster, respectively; D.H. performed bioinformatic analyses; M.L. and B.H. supervised the study and wrote the first draft of the manuscript; all authors discussed the results and commented on the manuscript.

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Correspondence to Mike Levine or Benjamin Haley.

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Supplementary Figures 1–7, Supplementary Tables 1–4 and Supplementary Methods (PDF 2219 kb)

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Shi, W., Hendrix, D., Levine, M. et al. A distinct class of small RNAs arises from pre-miRNA–proximal regions in a simple chordate. Nat Struct Mol Biol 16, 183–189 (2009). https://doi.org/10.1038/nsmb.1536

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