Strategy and tool for the identification of new microRNA-regulated genes by conserved targeting in plants

UCIEL CHOROSTECKI , JAVIER PALATNIK

Congreso; 4to. Congreso Argentino de Bioinformática y Biología Computacional (4CAB2C) y 4ta. Conferencia Internacional de la Sociedad Iberoamericana de Bioinformática (SolBio); 2013

Background MicroRNAs (miRNAs) are a class of small RNAs of 21 nt that are major regulators of gene expression in multicellular organisms. They recognize their targets by sequence complementarity and guide them to cleavage or translational arrest. Animal miRNAs have only limited complementarity to their targets and usually repress mRNA translation and accelerate their decay. In plants, miRNAs have an extended homology to their targets and frequently guide them to cleavage, although they can also inhibit their translation. While animal miRNAs regulate hundreds of targets with unclear biology, plant miRNAs act on much fewer genes. However, the regulation of each conserved target seems to be important for the biology of the plant. Their prediction usually relies on the use of empirical parameters deduced from known miRNA-target interactions. Many plant miRNAs are young small RNAs that have appeared recently during evolution, however their biological role is unclear. In contrast, ancient plant miRNAs play relevant functions in plant biology and regulate targets whose miRNA-binding sites are also conserved during evolution. This conservation, specially between arabidopsis and rice, has been used to support the prediction of targets based on empirical approaches, however it has not been fully exploited to identify new targets. Results We have developed a bioinformatic strategy and a web-tool for the identification of miRNA targets which is mainly based on the conservation of the potential regulation in different species. We applied the approach to transcript datasets from 37 plant species. The back-end carries out the searches, the integration of third-party tools that increases the specificity and sensitivity of the method and generates the results. The front-end is responsible for displaying the results with a user-friendly interface allowing the data analysis in several ways. To demonstrate the accuracy of the tool we predicted new targets that are conserved in a wide range of species, which likely implies that the interaction is biologically relevant. We experimentally validated some of them in Arabidopsis thaliana and found that miRNA targets might contain more mismatches than previously thought. Furthermore, we use this tool to predict and experimentally validate Solanaceae specific targets. Conclusions We designed a strategy and a web-tool that allows users to identify miRNA-regulated genes by focusing on the conservation of the potential targeting. We provided an alternative strategy to other predictions tools based solely on empirical parameters of known validated targets in plants. Furthermore, our tool allows adjusting the number of species requested as a filter to search with different sensitivities and signal-to-noise ratios.