Liu Shun, Li Jun-Hao, Wu Jie, Zhou Ke-Ren, Zhou Hui, Yang Jian-Hua, Qu Liang-Hu
Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, P. R. China.
Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, P. R. China State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P. R. China
Nucleic Acids Res. 2015 Jul 1;43(W1):W480-6. doi: 10.1093/nar/gkv524. Epub 2015 May 18.
Endogenous small non-coding RNAs (sRNAs), including microRNAs, PIWI-interacting RNAs and small interfering RNAs, play important gene regulatory roles in animals and plants by pairing to the protein-coding and non-coding transcripts. However, computationally assigning these various sRNAs to their regulatory target genes remains technically challenging. Recently, a high-throughput degradome sequencing method was applied to identify biologically relevant sRNA cleavage sites. In this study, an integrated web-based tool, StarScan (sRNA target Scan), was developed for scanning sRNA targets using degradome sequencing data from 20 species. Given a sRNA sequence from plants or animals, our web server performs an ultrafast and exhaustive search for potential sRNA-target interactions in annotated and unannotated genomic regions. The interactions between small RNAs and target transcripts were further evaluated using a novel tool, alignScore. A novel tool, degradomeBinomTest, was developed to quantify the abundance of degradome fragments located at the 9-11th nucleotide from the sRNA 5' end. This is the first web server for discovering potential sRNA-mediated RNA cleavage events in plants and animals, which affords mechanistic insights into the regulatory roles of sRNAs. The StarScan web server is available at http://mirlab.sysu.edu.cn/starscan/.
内源性小非编码RNA（sRNA），包括微小RNA、PIWI相互作用RNA和小干扰RNA，通过与蛋白质编码和非编码转录本配对，在动植物中发挥重要的基因调控作用。然而，通过计算将这些不同的sRNA与其调控靶基因进行匹配在技术上仍然具有挑战性。最近，一种高通量降解组测序方法被用于识别生物学上相关的sRNA切割位点。在本研究中，开发了一种基于网络的集成工具StarScan（sRNA靶标扫描），用于使用来自20个物种的降解组测序数据扫描sRNA靶标。给定来自植物或动物的sRNA序列，我们的网络服务器会在注释和未注释的基因组区域中对潜在的sRNA-靶标相互作用进行超快速且详尽的搜索。使用一种新型工具alignScore进一步评估小RNA与靶转录本之间的相互作用。开发了一种新型工具degradomeBinomTest，用于量化位于sRNA 5'端第9至11个核苷酸处的降解组片段的丰度。这是第一个用于发现动植物中潜在的sRNA介导的RNA切割事件的网络服务器，它为sRNA的调控作用提供了机制上的见解。StarScan网络服务器可在http://mirlab.sysu.edu.cn/starscan/上获取。
