miR-EdiTar: a database of predicted A-to-I edited miRNA target sites

Abstract

Motivation: A-to-I RNA editing is an important mechanism that consists of the conversion of specific adenosines into inosines in RNA molecules. Its dysregulation has been associated to several human diseases including cancer. Recent work has demonstrated a role for A-to-I editing in microRNA (miRNA)-mediated gene expression regulation. In fact, edited forms of mature miRNAs can target sets of genes that differ from the targets of their unedited forms. The specific deamination of mRNAs can generate novel binding sites in addition to potentially altering existing ones.

Results: This work presents miR-EdiTar, a database of predicted A-to-I edited miRNA binding sites. The database contains predicted miRNA binding sites that could be affected by A-to-I editing and sites that could become miRNA binding sites as a result of A-to-I editing.

Availability: miR-EdiTar is freely available online at http://microrna.osumc.edu/mireditar.

Contact: alessandro.lagana@osumc.edu or carlo.croce@osumc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Examples of predicted miRNA binding sites potentially affected by A-to-I editing. (a) Predicted binding site for miR-511 in the 3′ UTR of CTSS. (b) An edited adenosine in a potential binding site for miR-324-5p on the 3′ UTR of MRI1 may improve the seed match by adding an extra CG bond and changing the type from 7mer-A1 to 8mer. (c) An example of variation of structural accessibility of predicted miRNA binding sites affected by A-to-I editing. The estimated structural accessibility of a predicted binding site for miR-590-3p in the 3′ UTR of the gene ARHGAP26 decreases by 40% due to editing events. The predicted interactions are shown along with the secondary structures of the unedited and edited versions of the binding sites