miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii

Abstract

MicroRNAs (miRNAs) in eukaryotes guide post-transcriptional regulation by means of targeted RNA degradation and translational arrest1. They are released by a Dicer nuclease as a 21–24-nucleotide RNA duplex from a precursor in which an imperfectly matched inverted repeat forms a partly double-stranded region. One of the two strands is then recruited by an Argonaute nuclease that is the effector protein of the silencing mechanism. Short interfering RNAs (siRNAs), which are similar to miRNAs, are also produced by Dicer but the precursors are perfectly double-stranded RNA. These siRNAs guide post-transcriptional regulation, as with miRNAs, and epigenetic genome modification. Diverse eukaryotes including fungi, plants, protozoans and metazoans produce siRNAs2,3,4,5 but, until now, miRNAs have not been described in unicellular organisms and it has been suggested that they evolved together with multicellularity in separate plant and animal lineages6. Here we show that the unicellular alga Chlamydomonas reinhardtii contains miRNAs, putative evolutionary precursors of miRNAs and species of siRNAs resembling those in higher plants. The common features of miRNAs and siRNAs in an alga and in higher plants indicate that complex RNA-silencing systems evolved before multicellularity and were a feature of primitive eukaryotic cells.

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Figure 1: Chlamydomonas sRNAs.
Figure 2: Phasing siRNA loci in Chlamydomonas.
Figure 3: Chlamydomonas miRNAs.
Figure 4: miRNA action and protection.

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Acknowledgements

We thank S. Purton for helpful discussions and technical advice, and E. Havecker and R. A. Mosher for critical comments on the manuscript. This work was supported by the Gatsby Charitable Foundation. A.M. was a recipient of a long-term EMBO fellowship. F.S. was supported in part by a BBSRC grant and E.C.T. was supported by a Marie Curie Early Stage Training Fellowship. The Chlamydomonas genome sequence data were produced by the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/) and are provided for use in this publication only.

Author Contributions A.M. and D.C.B. designed research. A.M. and E.C.T. performed the experiments. F.S. and D.J.S. developed the sRNA pipeline and performed the computational analyses. A.M., F.S., D.J.S. and D.C.B. analysed the data. A.M., F.S. and D.C.B. wrote the paper.

The small RNA sequences have been deposited in GEO with the accession number GSE7575.

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Correspondence to David C. Baulcombe.

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This file contains Supplementary Tables 1-6 with Legends, Supplementary Figures 1-8 with Legends and Supplementary Notes (PDF 7927 kb)

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Molnár, A., Schwach, F., Studholme, D. et al. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 447, 1126–1129 (2007). https://doi.org/10.1038/nature05903

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