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Mirnasong: a Web-Based Tool for Generation and Testing of Mirna Sponge Constructs in Silico

Scientific reports(2016)SCI 3区

International Clinical Research Center | Department of Histology and Embryology

Cited 54|Views5
Abstract
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. URL: http://www.med.muni.cz/histology/miRNAsong/ .
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Key words
Antagomir and RNA sponge,High-throughput screening,miRNAs,Science,Humanities and Social Sciences,multidisciplinary
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要点】:本文介绍了一种名为miRNAsong的网页工具,用于miRNA海绵结构的生成和计算机辅助测试,提高了miRNA海绵设计的准确性和效率。

方法】:miRNAsong通过构建针对特定miRNA及其家族/簇的多个高亲和力结合位点,生成miRNA海绵结构,并在219个物种的35,828个miRNA序列中进行潜在结合测试。

实验】:作者利用miRNAsong设计并测试了针对miR-145的海绵结构,通过将其序列克隆入可诱导的慢病毒载体,并在表达miR-145海绵的细胞系中实验验证了其对miR-145的抑制效果,实验数据证明了miRNAsong工具的有效性。