PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing.
PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing.
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DOI：
10.1093/nar/gks277
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发表时间：
2012-07
影响因子：
14.9
通讯作者：
Moulton V
中科院分区：
文献类型：
--
作者：
Folkes L;Moxon S;Woolfenden HC;Stocks MB;Szittya G;Dalmay T;Moulton V
小RNA(SRNAs)是一类短的(20-25 -NT)非编码RNA，在基因表达中起着重要的调节作用。理解其功能的关键第一步是自信地识别sRNA靶标。在植物中，几类sRNAs，如microRNAs(MiRNAs)和反式作用的小干扰RNAs被证明与其信使RNA(MRNA)靶标具有近乎完美的互补性，通常导致信使RNA的切割。最近，一种被称为RNA末端平行分析(PARE)的高通量技术使大规模测定mRNA切割产物的序列成为可能。现在已经有了计算方法来使用这些数据来寻找保守的和新发现的miRNAs的靶标。由于速度的限制，这种方法依赖于用户知道哪些sRNA序列可能针对转录本。通过将搜索限制在sRNA的一个很小的子集上，很可能会错过许多其他sRNA/mRNA的相互作用。在这里，我们描述了一个新的软件工具，称为PAREsnip，它允许用户搜索从高通量测序实验中获得的所有sRNA的潜在目标。通过搜索完整的‘sRNAome’的靶标，我们可以促进大规模识别sRNA靶标，使我们能够发现调控相互作用网络。
Small RNAs (sRNAs) are a class of short (20–25 nt) non-coding RNAs that play important regulatory roles in gene expression. An essential first step in understanding their function is to confidently identify sRNA targets. In plants, several classes of sRNAs such as microRNAs (miRNAs) and trans-acting small interfering RNAs have been shown to bind with near-perfect complementarity to their messenger RNA (mRNA) targets, generally leading to cleavage of the mRNA. Recently, a high-throughput technique known as Parallel Analysis of RNA Ends (PARE) has made it possible to sequence mRNA cleavage products on a large-scale. Computational methods now exist to use these data to find targets of conserved and newly identified miRNAs. Due to speed limitations such methods rely on the user knowing which sRNA sequences are likely to target a transcript. By limiting the search to a tiny subset of sRNAs it is likely that many other sRNA/mRNA interactions will be missed. Here, we describe a new software tool called PAREsnip that allows users to search for potential targets of all sRNAs obtained from high-throughput sequencing experiments. By searching for targets of a complete ‘sRNAome’ we can facilitate large-scale identification of sRNA targets, allowing us to discover regulatory interaction networks.
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影响因子：
14.9
作者：
Kozomara A;Griffiths-Jones S
通讯作者：
Griffiths-Jones S
影响因子：
3.7
作者：
Fahlgren N;Howell MD;Kasschau KD;Chapman EJ;Sullivan CM;Cumbie JS;Givan SA;Law TF;Grant SR;Dangl JL;Carrington JC
通讯作者：
Carrington JC
影响因子：
9.2
作者：
Addo-Quaye, Charles;Eshoo, Tifani W.;Axtell, Michael J.
通讯作者：
Axtell, Michael J.
影响因子：
7.2
作者：
Li, Feng;Orban, Ryan;Baker, Barbara
通讯作者：
Baker, Barbara
影响因子：
5.8
作者：
Addo-Quaye, Charles;Miller, Webb;Axtell, Michael J.
通讯作者：
Axtell, Michael J.