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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00159816%3A_____%2F16%3A00065979" target="_blank" >RIV/00159816:_____/16:00065979 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14110/16:00088493

Result on the web

<a href="http://dx.doi.org/10.1038/srep36625" target="_blank" >http://dx.doi.org/10.1038/srep36625</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1038/srep36625" target="_blank" >10.1038/srep36625</a>

Result language

angličtina

Original language name

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

Original language description

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.

Czech name

—

Czech description

—

Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CE - Biochemistry

OECD FORD branch

—

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2016

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Scientific Reports

ISSN

2045-2322

e-ISSN

—

Volume of the periodical

6

Issue of the periodical within the volume

NOV

Country of publishing house

GB - UNITED KINGDOM

Number of pages

8

Pages from-to

36625

UT code for WoS article

000388072000001

EID of the result in the Scopus database

—