Experimental capture of miRNA targetomes: disease-specific 3′UTR library-based miRNA targetomics for Parkinson’s disease

The identification of targetomes remains a challenge given the pleiotropic effect of miRNAs, the limited effects of miRNAs on individual targets, and the sheer number of estimated miRNA–target gene interactions (MTIs), which is around 44,571,700. Currently, targetome identification for single miRNAs relies on computational evidence and functional studies covering smaller numbers of targets. To ensure that the targetome analysis could be experimentally verified by functional assays, we employed a systematic approach and explored the targetomes of four miRNAs (miR-129-5p, miR-129-1-3p, miR-133b, and miR-873-5p) by analyzing 410 predicted target genes, both of which were previously associated with Parkinson’s disease (PD). After performing 13,536 transfections, we validated 442 of the 705 putative MTIs (62,7%) through dual luciferase reporter assays. These analyses increased the number of validated MTIs by at least 2.1-fold for miR-133b and by a maximum of 24.3-fold for miR-873-5p. Our study contributes to the experimental capture of miRNA targetomes by addressing i) the ratio of experimentally verified MTIs to predicted MTIs, ii) the sizes of disease-related miRNA targetomes, and iii) the density of MTI networks. A web service to support the analyses on the MTI level is available online ( https://ccb-web.cs.uni-saarland.de/utr-seremato ), and all the data have been added to the miRATBase database ( https://ccb-web.cs.uni-saarland.de/miratbase ). This research aimed to explore the relationship between microRNAs and target genes, key to understanding molecular signals in diseases like Parkinson’s disease. The scientists used a method involving a collection of resources to identify potential interactions between microRNAs and their target genes in PD. They chose four microRNAs linked with PD and found 705 potential interactions. Using a partly automated test, they confirmed 442 of these interactions. The research also discovered that the effectiveness of microRNAs differs among various signal pathways. The results suggest that the local secondary structure of the miRNA binding site within the 3’ untranslated region of the target gene has a limited effect on the tests. This study lays the groundwork for further testing of potential interactions in specific disease characteristics. The results could impact the creation of microRNA-based treatments. This summary was initially drafted using artificial intelligence, then revised and fact-checked by the author.