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@article{1366170,
author = {Bárta, Tomáš and Pešková, Lucie and Hampl, Aleš},
article_location = {London},
article_number = {"neuvedeno"},
doi = {http://dx.doi.org/10.1038/srep36625},
keywords = {MICRORNA TARGET RECOGNITION; EMBRYONIC STEM-CELLS; CUMATE GENE-SWITCH; MAMMALIAN-CELLS; C-MYC; LENTIVIRAL VECTORS; MIR-145; CANCER; EXPRESSION; PREDICTION},
language = {eng},
issn = {2045-2322},
journal = {Scientific Reports},
title = {miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico},
volume = {6},
year = {2016}
}
TY - JOUR
ID - 1366170
AU - Bárta, Tomáš - Pešková, Lucie - Hampl, Aleš
PY - 2016
TI - miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico
JF - Scientific Reports
VL - 6
IS - "neuvedeno"
SP - 1-8
EP - 1-8
PB - Nature Publishing Group
SN - 20452322
KW - MICRORNA TARGET RECOGNITION
KW - EMBRYONIC STEM-CELLS
KW - CUMATE GENE-SWITCH
KW - MAMMALIAN-CELLS
KW - C-MYC
KW - LENTIVIRAL VECTORS
KW - MIR-145
KW - CANCER
KW - EXPRESSION
KW - PREDICTION
N2 - MicroRNA (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 introduce microRNA sponge generator and tester (miRNAsong), a freely available web-based tool for generation and in silico testing 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.
ER -
BÁRTA, Tomáš, Lucie PEŠKOVÁ and Aleš HAMPL. miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico. \textit{Scientific Reports}. London: Nature Publishing Group, 2016, vol.~6, ''neuvedeno'', p.~1-8. ISSN~2045-2322. Available from: https://dx.doi.org/10.1038/srep36625.
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