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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.

References

  1. 1

    Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004)

    CAS  Article  Google Scholar 

  2. 2

    Reinhart, B. J. & Bartel, D. P. Small RNAs correspond to centromere heterochromatic repeats. Science 297, 1831 (2002)

    CAS  Article  Google Scholar 

  3. 3

    Llave, C., Kasschau, K. D., Rector, M. A. & Carrington, J. C. Endogenous and silencing-associated small RNAs in plants. Plant Cell 14, 1605–1619 (2002)

    CAS  Article  Google Scholar 

  4. 4

    Djikeng, A., Shi, H. F., Tschudi, C. & Ullu, E. RNA interference in Trypanosoma brucei: Cloning of small interfering RNAs provides evidence for retroposon-derived 24- 26-nucleotide RNAs. RNA 7, 1522–1530 (2001)

    CAS  PubMed  PubMed Central  Google Scholar 

  5. 5

    Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T. & Jewell, D. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13, 807–818 (2003)

    CAS  Article  Google Scholar 

  6. 6

    Allen, E. et al. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nature Genet. 36, 1282–1290 (2004)

    CAS  Article  Google Scholar 

  7. 7

    Cerutti, H. & Casas-Mollano, J. A. On the origin and functions of RNA-mediated silencing: from protists to man. Curr. Genet. 50, 81–99 (2006)

    CAS  Article  Google Scholar 

  8. 8

    Lu, C. et al. MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res. 16, 1276–1288 (2006)

    CAS  Article  Google Scholar 

  9. 9

    Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208 (2003)

    CAS  Article  Google Scholar 

  10. 10

    Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209–216 (2003)

    CAS  Article  Google Scholar 

  11. 11

    Vazquez, F. et al. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell 16, 69–79 (2004)

    CAS  Article  Google Scholar 

  12. 12

    Borsani, O., Zhu, J., Verslues, P. E., Sunkar, R. & Zhu, J.-K. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123, 1279–1291 (2005)

    CAS  Article  Google Scholar 

  13. 13

    Peragine, A., Yoshikawa, M., Wu, G., Albrecht, H. L. & Poethig, R. S. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev. 18, 2368–2379 (2004)

    CAS  Article  Google Scholar 

  14. 14

    Han, J. et al. Molecular basis for the recognition of primary micro-RNAs by the Drosha–DGCR8 complex. Cell 125, 887–901 (2006)

    CAS  Article  Google Scholar 

  15. 15

    Llave, C., Xie, Z., Kasschau, K. D. & Carrington, J. C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297, 2053–2056 (2002)

    ADS  CAS  Article  Google Scholar 

  16. 16

    Schwab, R. et al. Specific effects of microRNAs on the plant transcriptome. Dev. Cell 8, 517–527 (2005)

    CAS  Article  Google Scholar 

  17. 17

    Pazour, G. J., Agrin, N., Leszyk, J. & Witman, G. B. Proteomic analysis of a eukaryotic cilium. J. Cell Biol. 170, 103–113 (2005)

    CAS  Article  Google Scholar 

  18. 18

    Yu, B. et al. Methylation as a crucial step in plant microRNA biogenesis. Science 307, 932–935 (2005)

    ADS  CAS  Article  Google Scholar 

  19. 19

    Yang, Z., Ebright, Y. W., Yu, B. & Chen, X. HEN1 recognizes 21–24 nt small RNA duplexes and deposits a methyl group onto the 2′ OH of the 3′ terminal nucleotide. Nucleic Acids Res. 34, 667–675 (2006)

    CAS  Article  Google Scholar 

  20. 20

    Li, J., Yang, Z., Yu, B., Liu, J. & Chen, X. Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr. Biol. 15, 1501–1507 (2005)

    CAS  Article  Google Scholar 

  21. 21

    Floyd, S. K. & Bowman, J. L. Ancient microRNA target sequences in plants. Nature 428, 485–486 (2004)

    ADS  CAS  Article  Google Scholar 

  22. 22

    Arazi, T. et al. Cloning and characterization of micro-RNAs from moss. Plant J. 43, 837–848 (2005)

    CAS  Article  Google Scholar 

  23. 23

    Baulcombe, D. RNA silencing in plants. Nature 431, 356–363 (2004)

    ADS  CAS  Article  Google Scholar 

  24. 24

    Wegener, D., Treier, U. & Beck, C. F. Procedures for the generation of mature Chlamydomonas reinhardtii zygotes for molecular and biochemical analyses. Plant Physiol. 90, 512–515 (1989)

    CAS  Article  Google Scholar 

  25. 25

    Chappell, L., Baulcombe, D. & Molnar, A. in Current Protocols in Microbiology (eds Coico, R. et al.) 16H.2.1–16H.2.17 (Wiley, Hoboken, NJ, 2005)

    Google Scholar 

  26. 26

    Baumberger, N. & Baulcombe, D. C. Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits micro RNAs and short interfering RNAs. Proc. Natl Acad. Sci. USA 102, 11928–11933 (2005)

    ADS  CAS  Article  Google Scholar 

  27. 27

    Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005)

    ADS  CAS  Article  Google Scholar 

  28. 28

    Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 1–19 (2004)

    Article  Google Scholar 

  29. 29

    Hofacker, I. L. et al. Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125, 167–188 (1994)

    CAS  Article  Google Scholar 

  30. 30

    Bonnet, E., Wuyts, J., Rouze, P. & Van de Peer, Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20, 2911–2917 (2004)

    CAS  Article  Google Scholar 

Download references

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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