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Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana

Nature Genetics volume 36, pages 12821290 (2004) | Download Citation

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Abstract

MicroRNAs (miRNAs) in plants and animals function as post-transcriptional regulators of target genes, many of which are involved in multicellular development. miRNAs guide effector complexes to target mRNAs through base-pair complementarity, facilitating site-specific cleavage or translational repression. Biogenesis of miRNAs involves nucleolytic processing of a precursor transcript with extensive foldback structure. Here, we provide evidence that genes encoding miRNAs in plants originated by inverted duplication of target gene sequences. Several recently evolved genes encoding miRNAs in Arabidopsis thaliana and other small RNA–generating loci possess the hallmarks of inverted duplication events that formed the arms on each side of their respective foldback precursors. We propose a model for miRNA evolution that suggests a mechanism for de novo generation of new miRNA genes with unique target specificities.

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Acknowledgements

We thank S. Givan, D. Smith and C. Sullivan for assistance and advice with computational resources; L. Johansen for initial propagation of the rdr6-15 mutant; and S. Poethig and H. Vaucheret for discussions about trans-acting siRNAs and the suggestion to analyze miR161 in multiple dcl1 mutated alleles. This work was supported by grants from the US National Science Foundation, the US National Institutes of Health and the United States Department of Agriculture.

Author information

Affiliations

  1. Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA.

    • Edwards Allen
    • , Zhixin Xie
    • , Adam M Gustafson
    •  & James C Carrington
  2. Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA.

    • Edwards Allen
    • , Zhixin Xie
    • , Adam M Gustafson
    • , Gi-Ho Sung
    • , Joseph W Spatafora
    •  & James C Carrington

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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to James C Carrington.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    Predicted foldback structures for small RNA generating loci containing inverted repeats with similarity to protein coding genes.

Excel files

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    Supplementary Table 1

    MIRNA genes and small RNA-generating loci used for FASTA searches presented in Figure 2.

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DOI

https://doi.org/10.1038/ng1478

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