Abstract
BackgroundIn many eukaryotes, microRNAs (miRNAs) bind to complementary sites in the 3'-untranslated regions (3'-UTRs) of target messenger RNAs (mRNAs) and regulate their expression at the stage of translation. Recent studies have revealed that many miRNAs are evolutionarily conserved; however, the evolution of their target genes has yet to be systematically characterized. We sought to elucidate a set of conserved miRNA/target-gene pairs and to analyse the mechanism underlying miRNA-mediated gene regulation in the early stage of bilaterian evolution.ResultsInitially, we extracted five evolutionarily conserved miRNAs (let-7, miR-1, miR-124, miR-125/lin-4, and miR-34) among five diverse bilaterian animals. Subsequently, we designed a procedure to predict evolutionarily conserved miRNA/target-gene pairs by introducing orthologous gene information. As a result, we extracted 31 orthologous miRNA/target-gene pairs that were conserved among at least four diverse bilaterian animals; the prediction set showed prominent enrichment of orthologous miRNA/target-gene pairs that were verified experimentally. Approximately 84% of the target genes were regulated by three miRNAs (let-7, miR-1, and miR-124) and their function was classified mainly into the following categories: development, muscle formation, cell adhesion, and gene regulation. We used a reporter gene assay to experimentally verify the downregulation of six candidate pairs (out of six tested pairs) in HeLa cells.ConclusionsThe application of our new method enables the identification of 31 miRNA/target-gene pairs that were expected to have been regulated from the era of the common bilaterian ancestor. The downregulation of all six candidate pairs suggests that orthologous information contributed to the elucidation of the primordial set of genes that has been regulated by miRNAs; it was also an efficient tool for the elimination of false positives from the predicted candidates. In conclusion, our study identified potentially important miRNA-target pairs that were evolutionarily conserved throughout diverse bilaterian animals and that may provide new insights into early-stage miRNA functions.
Highlights
In many eukaryotes, microRNAs bind to complementary sites in the 3’-untranslated regions (3’-UTRs) of target messenger RNAs and regulate their expression at the stage of translation
Gallus, D. melanogaster, and C. elegans) among bilaterian animals, for which there exists a vast array of data on both miRNAs and messenger RNAs (mRNAs) [13]
Huang et al described the extraction of 15 conserved miRNA families among six bilaterian animals (H. sapiens, M. musculus, G. gallus, D. rerio, D. melanogaster, and C. elegans) based on their original classification method [24], which included our five miRNA families
Summary
MicroRNAs (miRNAs) bind to complementary sites in the 3’-untranslated regions (3’-UTRs) of target messenger RNAs (mRNAs) and regulate their expression at the stage of translation. MicroRNAs (miRNAs) are a class of short (18-25 nucleotides) non-coding RNAs that regulate gene expression posttranscriptionally Their regulatory potential relies heavily on the recognition of binding sites that are located mainly in the 3’-untranslated regions (3’-UTRs) of target messenger RNAs (mRNAs) [1]. In a recent report by Friedman et al, the expression of a large number of target genes is predicted to be regulated by miRNAs [14]; relatively few of these have been verified experimentally To overcome this problem, a series of computational methods has been developed to predict a large number of miRNA targets; e.g., TargetScan [14], RNAhybrid [15], MicroTar [16], PITA [17], miRanda [18], and PicTar [19]. As for miRNAs, many miRNA families are found among various bilaterian animals, suggesting that several miRNAs and their target genes may have co-evolved; these features have yet to be systematically characterized
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
