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bioRxiv · 10.1101/2021.06.16.448293

scanMiR: a biochemically-based toolkit for versatile and efficient microRNA target prediction

Soutschek, M.·Gross, F.·Schratt, G.·Germain, P.-L.
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Abstract

microRNAs are important post-transcriptional regulators of gene expression, but the identification of functionally relevant targets is still challenging. Recent research has shown improved prediction of microRNA-mediated repression using a biochemical model combined with empirically-derived k-mer affinity predictions. Here, we translate this approach into a flexible and user-friendly bioconductor package, scanMiR, also available through a web interface. Using lightweight linear models, scanMiR efficiently scans for binding sites, estimates their affinity, and predicts aggregated transcript repression. Moreover, flexible 3-supplementary alignment enables the prediction of unconventional interactions, such as bindings potentially leading to target-directed microRNA degradation (TDMD) or slicing. We showcase scanMiR through a systematic scan for such unconventional sites on neuronal transcripts, including lncRNAs and circRNAs.

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Soutschek, M., Gross, F., Schratt, G., Germain, P.-L.. 2021-06-17. scanMiR: a biochemically-based toolkit for versatile and efficient microRNA target prediction. https://doi.org/10.1101/2021.06.16.448293

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