miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico

Tomas Barta; Lucie Peskova; Ales Hampl

doi:10.1038/srep36625

journal article Open Access Nov 18, 2016

miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico

Tomas Barta

Lucie Peskova

Ales Hampl

Scientific Reports Vol. 6 No. 1 · Springer Science and Business Media LLC

View at Publisher Save 10.1038/srep36625

Abstract

AbstractMicroRNA (miRNA) sponges are RNA transcripts containing multiple high-affinity binding sites that associate with and sequester specific miRNAs to prevent them from interacting with their target messenger (m)RNAs. Due to the high specificity of miRNA sponges and strong inhibition of target miRNAs, these molecules have become increasingly applied in miRNA loss-of-function studies. However, improperly designed sponge constructs may sequester off-target miRNAs; thus, it has become increasingly important to develop a tool for miRNA sponge construct design and testing. In this study, we introducemicroRNA spongegenerator and tester (miRNAsong), a freely available web-based tool for generation andin silicotesting of miRNA sponges. This tool generates miRNA sponge constructs for specific miRNAs and miRNA families/clusters and tests them for potential binding to miRNAs in selected organisms. Currently, miRNAsong allows for testing of sponge constructs in 219 species covering 35,828 miRNA sequences. Furthermore, we also provide an example, supplemented with experimental data, of how to use this tool. Using miRNAsong, we designed and tested a sponge for miR-145 inhibition, and cloned the sequence into an inducible lentiviral vector. We found that established cell lines expressing miR-145 sponge strongly inhibited miR-145, thus demonstrating the usability of miRNAsong tool for sponge generation. URL:http://www.med.muni.cz/histology/miRNAsong/.

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Published: Nov 18, 2016
Vol/Issue: 6(1)
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Cite This Article

Tomas Barta, Lucie Peskova, Ales Hampl (2016). miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico. Scientific Reports, 6(1). https://doi.org/10.1038/srep36625

miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico

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