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Intronic microRNA precursors that bypass Drosha processing

Nature volume 448, pages 83–86 (2007)Cite this article

Abstract

MicroRNAs (miRNAs) are ∼22-nucleotide endogenous RNAs that often repress the expression of complementary messenger RNAs1. In animals, miRNAs derive from characteristic hairpins in primary transcripts through two sequential RNase III-mediated cleavages; Drosha cleaves near the base of the stem to liberate a ∼60-nucleotide pre-miRNA hairpin, then Dicer cleaves near the loop to generate a miRNA:miRNA* duplex2,3. From that duplex, the mature miRNA is incorporated into the silencing complex. Here we identify an alternative pathway for miRNA biogenesis, in which certain debranched introns mimic the structural features of pre-miRNAs to enter the miRNA-processing pathway without Drosha-mediated cleavage. We call these pre-miRNAs/introns ‘mirtrons’, and have identified 14 mirtrons in Drosophila melanogaster and another four in Caenorhabditis elegans (including the reclassification of mir-62). Some of these have been selectively maintained during evolution with patterns of sequence conservation suggesting important regulatory functions in the animal. The abundance of introns comparable in size to pre-miRNAs appears to have created a context favourable for the emergence of mirtrons in flies and nematodes. This suggests that other lineages with many similarly sized introns probably also have mirtrons, and that the mirtron pathway could have provided an early avenue for the emergence of miRNAs before the advent of Drosha.

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Figure 1: Introns that form pre-miRNAs.
Figure 2: Mirtrons are spliced as introns and diced as pre-miRNAs.
Figure 3: Emergence and conservation of mirtrons in species with appropriately sized introns.

References

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

    Article  CAS  Google Scholar 

  2. Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419 (2003)

    Article  ADS  CAS  Google Scholar 

  3. Tomari, Y. & Zamore, P. D. Perspective: machines for RNAi. Genes Dev. 19, 517–529 (2005)

    Article  CAS  Google Scholar 

  4. Ruby, J. G. et al. Biogenesis, expression, and target predictions for an expanded set of microRNA genes in Drosophila. Genome Res. (in the press)

  5. Ruby, J. G. et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127, 1193–1207 (2006)

    Article  CAS  Google Scholar 

  6. Lim, L. P. et al. The microRNAs of Caenorhabditis elegans. Genes Dev. 17, 991–1008 (2003)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  8. Ruskin, B. & Green, M. R. An RNA processing activity that debranches RNA lariats. Science 229, 135–140 (1985)

    Article  ADS  CAS  Google Scholar 

  9. Padgett, R. A., Konarska, M. M., Grabowski, P. J., Hardy, S. F. & Sharp, P. A. Lariat RNA's as intermediates and products in the splicing of messenger RNA precursors. Science 225, 898–903 (1984)

    Article  ADS  CAS  Google Scholar 

  10. Hutvagner, G. et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293, 834–838 (2001)

    Article  CAS  Google Scholar 

  11. Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858–862 (2001)

    Article  ADS  CAS  Google Scholar 

  12. Lim, L. P. & Burge, C. B. A computational analysis of sequence features involved in recognition of short introns. Proc. Natl Acad. Sci. USA 98, 11193–11198 (2001)

    Article  ADS  CAS  Google Scholar 

  13. Lo, P. C., Roy, D. & Mount, S. M. Suppressor U1 snRNAs in Drosophila. Genetics 138, 365–378 (1994)

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Kim, Y. K. & Kim, V. N. Processing of intronic microRNAs. EMBO J. 26, 775–783 (2007)

    Article  CAS  Google Scholar 

  15. Yandell, M. et al. Large-scale trends in the evolution of gene structures within 11 animal genomes. PLoS Comput. Biol. 2, e15 (2006)

    Article  ADS  Google Scholar 

  16. Lee, R. C. & Ambros, V. An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862–864 (2001)

    Article  ADS  CAS  Google Scholar 

  17. Griffiths-Jones, S. The microRNA registry. Nucleic Acids Res. 32, D109–D111 (2004)

    Article  CAS  Google Scholar 

  18. Leverette, R. D., Andrews, M. T. & Maxwell, E. S. Mouse U14 snRNA is a processed intron of the cognate hsc70 heat shock pre-messenger RNA. Cell 71, 1215–1221 (1992)

    Article  CAS  Google Scholar 

  19. Grumbling, G. & Strelets, V. FlyBase: anatomical data, images and queries. Nucleic Acids Res. 34, D484–D488 (2006)

    Article  CAS  Google Scholar 

  20. Stein, L., Sternberg, P., Durbin, R., Thierry-Mieg, J. & Spieth, J. WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 29, 82–86 (2001)

    Article  CAS  Google Scholar 

  21. Pruitt, K. D., Tatusova, T. & Maglott, D. R. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 33, D501–D504 (2005)

    Article  CAS  Google Scholar 

  22. Karolchik, D. et al. The UCSC genome browser database. Nucleic Acids Res. 31, 51–54 (2003)

    Article  CAS  Google Scholar 

  23. Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185–2195 (2000)

    Article  Google Scholar 

  24. Richards, S. et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 15, 1–18 (2005)

    Article  CAS  Google Scholar 

  25. Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708–715 (2004)

    Article  CAS  Google Scholar 

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

    CAS  Google Scholar 

  27. Brennecke, J., Stark, A., Russell, R. B. & Cohen, S. M. Principles of microRNA-target recognition. PLoS Biol. 3, e85 (2005)

    Article  Google Scholar 

  28. Dorner, S. et al. A genomewide screen for components of the RNAi pathway in Drosophila cultured cells. Proc. Natl Acad. Sci. USA 103, 11880–11885 (2006)

    Article  ADS  CAS  Google Scholar 

  29. Forstemann, K. et al. Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol. 3, e236 (2005)

    Article  Google Scholar 

  30. Lim, L. P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769–773 (2005)

    Article  ADS  CAS  Google Scholar 

Download references

Acknowledgements

We are grateful to P. Sharp, T. Baker and members of the Bartel laboratory for discussions. We thank W. Johnston for assistance with molecular cloning, E. Lai for contributing small-RNA-derived cDNAs for sequencing, the Drosophila genome sequencing community and the UCSC genome browser staff for unpublished alignments, P. Zamore and R. Green for dsRNA plasmids, S. Cohen for GFP and firefly luciferase Drosophila expression plasmids, and D. Sabitini for pMT-puro. This work was supported by the NIH. C.H.J. is a NSF graduate research fellow. D.P.B. is an investigator of the Howard Hughes Medical Institute. Small RNA sequences were deposited in the Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo/), accessions GPL5061 and GSE7448.

Author Contributions J.G.R. performed the computational analysis. C.H.J. performed the experimental analysis. All authors contributed to the design of the study and preparation of the manuscript.

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Author notes

  1. J. Graham Ruby and Calvin H. Jan: These authors contributed equally to this work.

Authors and Affiliations

  1. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA,

    J. Graham Ruby, Calvin H. Jan & David P. Bartel

  2. Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA,

    J. Graham Ruby, Calvin H. Jan & David P. Bartel

Authors
  1. J. Graham Ruby
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  2. Calvin H. Jan
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Correspondence to David P. Bartel.

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Small RNA sequences were deposited in the Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo/), accessions GPL5061 and GSE7448. Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

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This file contains Supplementary Figures S1-S2 with Legends and Supplementary Tables S1-S4. (PDF 3538 kb)

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Ruby, J., Jan, C. & Bartel, D. Intronic microRNA precursors that bypass Drosha processing. Nature 448, 83–86 (2007). https://doi.org/10.1038/nature05983

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