Addo-Quaye Charles, Miller Webb, Axtell Michael J
Department of Computer Science and Engineering and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
Bioinformatics. 2009 Jan 1;25(1):130-1. doi: 10.1093/bioinformatics/btn604. Epub 2008 Nov 18.
MicroRNAs (miRNAs) are approximately 20- to 22-nt long endogenous RNA sequences that play a critical role in the regulation of gene expression in eukaryotic genomes. Confident identification of miRNA targets is vital to understand their functions. Currently available computational algorithms for miRNA target prediction have diverse degrees of sensitivity and specificity and as a consequence each predicted target generally requires experimental confirmation. miRNAs and other small RNAs that direct endonucleolytic cleavage of target mRNAs produce diagnostic uncapped, polyadenylated mRNA fragments. Degradome sequencing [also known as PARE (parallel analysis of RNA ends) and GMUCT (genome-wide mapping of uncapped transcripts)] samples the 5'-ends of uncapped mRNAs and can be used to discover in vivo miRNA targets independent of computational predictions. Here, we describe a generalizable computational pipeline, CleaveLand, for the detection of cleaved miRNA targets from degradome data. CleaveLand takes as input degradome sequences, small RNAs and an mRNA database and outputs small RNA targets. CleaveLand can thus be applied to degradome data from any species provided a set of mRNA transcripts and a set of query miRNAs or other small RNAs are available.
The code and documentation for CleaveLand is freely available under a GNU license at http://www.bio.psu.edu/people/faculty/Axtell/AxtellLab/Software.html
微小RNA(miRNA)是长度约为20至22个核苷酸的内源性RNA序列,在真核生物基因组的基因表达调控中起关键作用。准确鉴定miRNA靶标对于理解其功能至关重要。目前可用的用于miRNA靶标预测的计算算法具有不同程度的敏感性和特异性,因此每个预测的靶标通常都需要实验验证。引导靶标mRNA进行核酸内切酶切割的miRNA和其他小RNA会产生诊断性的无帽、多聚腺苷酸化的mRNA片段。降解组测序[也称为PARE(RNA末端平行分析)和GMUCT(无帽转录本的全基因组图谱)]对无帽mRNA的5'末端进行采样,可用于发现体内miRNA靶标,而无需依赖计算预测。在这里,我们描述了一种通用的计算流程CleaveLand,用于从降解组数据中检测被切割的miRNA靶标。CleaveLand将降解组序列、小RNA和mRNA数据库作为输入,并输出小RNA靶标。因此,只要有一组mRNA转录本以及一组查询miRNA或其他小RNA,CleaveLand就可以应用于任何物种的降解组数据。
CleaveLand的代码和文档可在GNU许可下从http://www.bio.psu.edu/people/faculty/Axtell/AxtellLab/Software.html免费获取。