Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important new target genes.

Bonnet, E., Wuyts, J., Rouzé, P., Van de Peer, Y.

Corresponding authors: ,

Abstract

MicroRNAs (miRNAs) are an extensive class of tiny RNA molecules that regulate the expression of target genes by means of complementary base pair interactions. Although the first miRNAs were discovered in Caenorhabditis elegans, >300 miRNAs were recently documented in animals and plants, both by cloning methods and computational predictions. We present a genome-wide computational approach to detect miRNA genes in the Arabidopsis thaliana genome. Our method is based on the conservation of short sequences between the genomes of Arabidopsis and rice (Oryza sativa) and on properties of the secondary structure of the miRNA precursor. The method was fine-tuned to take into account plant-specific properties, such as the variable length of the miRNA precursor sequences. In total, 91 potential miRNA genes were identified, of which 58 had at least one nearly perfect match with an Arabidopsis mRNA, constituting the potential targets of those miRNAs. In addition to already known transcription factors involved in plant development, the targets also comprised genes involved in several other cellular processes, such as sulfur assimilation and ubiquitin-dependent protein degradation. These findings considerably broaden the scope of miRNA functions in plants.

Supplementary Data

  1. Erratum (December, 15, 2004)
  2. Table 4 : miRNA_list_update.xls. Updated list of Arabidopsis candidate microRNAs, with a new nomenclature and false positives removed.< /p>

  3. Figures
  4. Figure 1: Six characteristic secondary structure features were extracted from a reference set of Arabidopsis thaliana miRNAs, do wnloaded from the RFAM database. Lateron in the analysis, these values were used as cutoff scores to validate miRNA precursor candi dates. The six features are: (a) The miRNA should be part of 1 continuous helix. (b) The minimum folding energy of the precursor sequence should be at least -30Kcal/mol (or more neg ative). (c) The sequence representing the mature miRNA should form at least 15 basepairs in the precursor sequence. (d) There must be no more than 5 unpaired bases in the miRNA or ( e) in the complementary strand. (We do not discriminate between internal loops and bulge loops). Finally, (f) there should be no more than 5 G:U base pairs in the sequence represent ing the mature miRNA.

    Figure 2: (PDF) Dendrogram showing the clustering of all miRNAs according to sequence similarity. More information is available in the man uscript.

    Figure 3: Eight of the miRNAs predicted by our pipeline target a number of genes of the ubiquitination pathway, with TIR1 as a typical member, which is targetted by MIR20. To validate prediction of MIR20, we found homologs with perfectly conserved miRNA sequences with a valid stem-loop precursor structure in three plants genomes, namely Medicago truncatula, Populus trichocarpa, and Lotus corniculatus.

  5. Tables
  6. Table 1: (Extended version) This table is an extended version of table 1 in the manuscript.

    Table 2: (MS Excel spreadsheet, OpenOffice.org spreadsheet) List of all 91 miRNAs, their sequence, location i n the genome and targets genes.

    Table 3: (MS Excel spreadsheet, OpenOffice.org spreadsheet) Matches between miRNAs and their target mRNAs.

  7. Data











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