CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets
CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets
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DOI：
10.1093/bioinformatics/btn604
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发表时间：
2009-01-01
期刊：
影响因子：
5.8
通讯作者：
Axtell, Michael J.
中科院分区：
文献类型：
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作者：
Addo-Quaye, Charles;Miller, Webb;Axtell, Michael J.
microRNA（miRNA）类似于20至22-NT长的内源性RNA序列，这些RNA序列在真核基因组中基因表达的调节中起关键作用。骗子。 miRNA靶标的凹痕鉴定对于了解其功能至关重要。当前可用的miRNA目标预测计算算法具有不同程度的灵敏度和特异性，因此每个预测目标通常都需要实验确认。靶mRNA的直接内核分解裂解的miRNA和其他小RNA会产生诊断性的，多腺苷酸化的mRNA片段。降解组测序[也称为PARE（RNA末端的平行分析）和Gmuct（无盖转录的全基因组映射）]样品样本未封闭的mRNA的5'端，可用于在体内miRNA目标中发现独立于计算预测的体内miRNA靶标。在这里，我们描述了可概括的计算管道Cleaveland，用于检测从降解组数据中裂解的miRNA靶标。 Cleaveland作为输入降解组序列，小RNA和mRNA数据库，并输出小的RNA靶标。因此，可以将Cleaveland应用于任何物种的降解组数据，只要一组mRNA转录本，并且可以使用一组查询miRNA或其他小型RNA。
MicroRNAs (miRNAs) are similar to 20- to 22-nt long endogenous RNA sequences that play a critical role in the regulation of gene expression in eukaryotic genomes. Con. dent 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.