spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.
spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.
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DOI：
10.1093/nar/gkw443
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发表时间：
2016-07-08
影响因子：
14.9
通讯作者：
Conesa A
中科院分区：
文献类型：
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作者：
Furió-Tarí P;Tarazona S;Gabaldón T;Enright AJ;Conesa A
非编码RNA转录物如microRNA（miRNAs）和长链非编码RNA（lncRNA）是重要的遗传调节因子。然而，许多这些转录本的功能仍然不清楚。最近，已经变得明显的是，在miRNA和lncRNA之间存在显著的串扰，并且这在miRNA、lncRNA和其他调节靶标之间产生结合的竞争。事实上，已经鉴定出各种竞争性内源性RNA（ceRNA），其中lncRNA通过隔离miRNA发挥作用。这意味着miRNA与其mRNA靶点相互作用的下调，即所谓的海绵效应。存在多种方法用于预测mRNA中的miRNA靶标。然而，很少有方法存在用于预测作为ceRNA（海绵）的lncRNA中的miRNA响应元件（MRE）。在这里，我们提出了spongeScan（spongescan.rc.ufl.edu），一个图形网络工具，用于计算和可视化lncRNA中假定的MRE，沿着不同的措施，以评估它们作为ceRNA的可能行为。
Non-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, it has become apparent that there is significant crosstalk between miRNAs and lncRNAs and that this creates competition for binding between the miRNA, a lncRNA and other regulatory targets. Indeed, various competitive endogenous RNAs (ceRNAs) have already been identified where a lncRNA acts by sequestering miRNAs. This implies the down-regulation in the interaction of the miRNAs with their mRNA targets, what has been called a sponge effect. Multiple approaches exist for the prediction of miRNA targets in mRNAs. However, few methods exist for the prediction of miRNA response elements (MREs) in lncRNAs acting as ceRNAs (sponges). Here, we present spongeScan (http://spongescan.rc.ufl.edu), a graphical web tool to compute and visualize putative MREs in lncRNAs, along with different measures to assess their likely behavior as ceRNAs.