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

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.

Fig. 1.

Overview of the mirfinder computational pipeline to detect miRNAs in plants. For details, see text.

Fig. 2.

RNA secondary structure models of the eight precursor molecules (four each from Arabidopsis and rice) of the miRNAs that target the 5′ UTR of the Arabidopsis gene At2g33770.1 and its rice homolog. The precursor molecules are drawn with the miRNAs aligned and highlighted in red. (Middle) The graph represents the Shannon entropy of the nucleotide content of each corresponding position on the 3′ strand of the precursors. A low value means that all molecules have the same nucleotide at that position, whereas a high value reflects little or no nucleotide conservation. The sequence divergence outside of the mature miRNA positions is clearly shown. RNA sequences are drawn from 5′ to 3′ in clockwise orientation. All precursors are truncated at the same position. RNA secondary structure drawings were made by using rnaviz (59).