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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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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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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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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DOI: https://doi.org/10.1038/nsmb.1536
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