CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs
CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs
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DOI：
10.1080/15476286.2015.1128065
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发表时间：
2016-01-02
期刊：
影响因子：
4.1
通讯作者：
Gorospe, Myriam
中科院分区：
文献类型：
--
作者：
Dudekulay, Dawood B.;Panda, Amaresh C.;Gorospe, Myriam
环状RNA（circRNA）在动物细胞中广泛表达，但其生物起源和功能尚不清楚。CircRNA已被证明是miRNA的海绵，也可能是潜在的海绵RNA结合蛋白（RBP），因此预测作为基因表达的强大转录后调节因子。大规模转录组数据的联合分析加上计算分析代表了一种强有力的方法来阐明核糖核蛋白（RNP）复合物可能的生物学作用。在这里，我们提出了一种新的网络工具CircInteractome（circRNA interactome），用于绘制人类circRNA上的RBP和miRNA结合位点。CircInteractome搜索公共circRNA、miRNA和RBP数据库，以提供circRNA上结合位点的生物信息学分析，并额外分析连接和连接侧翼序列上的miRNA和RBP位点。CircInteractome还使用户能够（1）识别可以充当RBP海绵的潜在CircRNA，（2）设计跨接头引物以特异性检测感兴趣的CircRNA，（3）设计用于CircRNA沉默的SiRNA，以及（4）识别潜在的内部核糖体进入位点（IRES）。总之，网络工具CircInteractome（可在http://circinteractome.nia.nih.gov上免费访问）促进了circRNA和circRNP生物学的分析。
Circular RNAs (circRNAs) are widely expressed in animal cells, but their biogenesis and functions are poorly understood. CircRNAs have been shown to act as sponges for miRNAs and may also potentially sponge RNA-binding proteins (RBPs) and are thus predicted to function as robust posttranscriptional regulators of gene expression. The joint analysis of large-scale transcriptome data coupled with computational analyses represents a powerful approach to elucidate possible biological roles of ribonucleoprotein (RNP) complexes. Here, we present a new web tool, CircInteractome (circRNA interactome), for mapping RBP- and miRNA-binding sites on human circRNAs. CircInteractome searches public circRNA, miRNA, and RBP databases to provide bioinformatic analyses of binding sites on circRNAs and additionally analyzes miRNA and RBP sites on junction and junction-flanking sequences. CircInteractome also allows the user the ability to (1) identify potential circRNAs which can act as RBP sponges, (2) design junction-spanning primers for specific detection of circRNAs of interest, (3) design siRNAs for circRNA silencing, and (4) identify potential internal ribosomal entry sites (IRES). In sum, the web tool CircInteractome, freely accessible at http://circinteractome.nia.nih.gov, facilitates the analysis of circRNAs and circRNP biology.