Yang Jian-Hua, Li Jun-Hao, Shao Peng, Zhou Hui, Chen Yue-Qin, Qu Liang-Hu
Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China.
Nucleic Acids Res. 2011 Jan;39(Database issue):D202-9. doi: 10.1093/nar/gkq1056. Epub 2010 Oct 30.
MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (sRNAs) that regulate gene expression by targeting messenger RNAs. However, assigning miRNAs to their regulatory target genes remains technically challenging. Recently, high-throughput CLIP-Seq and degradome sequencing (Degradome-Seq) methods have been applied to identify the sites of Argonaute interaction and miRNA cleavage sites, respectively. In this study, we introduce a novel database, starBase (sRNA target Base), which we have developed to facilitate the comprehensive exploration of miRNA-target interaction maps from CLIP-Seq and Degradome-Seq data. The current version includes high-throughput sequencing data generated from 21 CLIP-Seq and 10 Degradome-Seq experiments from six organisms. By analyzing millions of mapped CLIP-Seq and Degradome-Seq reads, we identified ∼1 million Ago-binding clusters and ∼2 million cleaved target clusters in animals and plants, respectively. Analyses of these clusters, and of target sites predicted by 6 miRNA target prediction programs, resulted in our identification of approximately 400,000 and approximately 66,000 miRNA-target regulatory relationships from CLIP-Seq and Degradome-Seq data, respectively. Furthermore, two web servers were provided to discover novel miRNA target sites from CLIP-Seq and Degradome-Seq data. Our web implementation supports diverse query types and exploration of common targets, gene ontologies and pathways. The starBase is available at http://starbase.sysu.edu.cn/.
微小RNA（miRNA）是一类重要的小型非编码RNA（sRNA），通过靶向信使RNA来调控基因表达。然而，将miRNA与其调控的靶基因进行匹配在技术上仍然具有挑战性。最近，高通量CLIP-Seq和降解组测序（Degradome-Seq）方法已分别用于鉴定AGO蛋白相互作用位点和miRNA切割位点。在本研究中，我们介绍了一个新的数据库starBase（sRNA靶标数据库），该数据库是我们为便于从CLIP-Seq和Degradome-Seq数据全面探索miRNA-靶标相互作用图谱而开发的。当前版本包含来自六种生物的21个CLIP-Seq和10个Degradome-Seq实验产生的高通量测序数据。通过分析数百万条比对的CLIP-Seq和Degradome-Seq reads，我们分别在动物和植物中鉴定出约100万个AGO结合簇和约200万个切割靶标簇。对这些簇以及6个miRNA靶标预测程序预测的靶位点进行分析，我们分别从CLIP-Seq和Degradome-Seq数据中鉴定出约40万个和约6.6万个miRNA-靶标调控关系。此外，还提供了两个网络服务器，用于从CLIP-Seq和Degradome-Seq数据中发现新的miRNA靶位点。我们的网络实现支持多种查询类型以及对共同靶标、基因本体和通路的探索。starBase可在http://starbase.sysu.edu.cn/获取。
