snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions
snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions
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DOI：
10.1016/j.gene.2007.10.037
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发表时间：
2008-01-31
期刊：
影响因子：
3.5
通讯作者：
Fedorov, Alexei
中科院分区：
文献类型：
--
作者：
Bazeley, Peter S.;Shepelev, Valery;Fedorov, Alexei
在人类中发现的数千种非蛋白质编码RNA中，一个重要的群体代表了引导其他类型RNA进行特定化学修饰、切割或正确折叠的snoRNA分子。然而，数百种哺乳动物snoRNA具有未知的功能，被称为“孤儿”分子。2006年，首次发现一种特殊的孤儿snoRNA（HBII-52）在人类和其他哺乳动物中5-羟色胺受体基因的选择性剪接调控中发挥重要作用。为了促进snoRNA可能参与前体mRNA加工调控的研究，我们开发了一个新的计算网络资源snoTARGET，它在人类和啮齿动物的外显子和内含子序列的整个集合中搜索snoRNA可能的指导位点。应用snoTARGET为许多人类和啮齿动物孤儿C/D-box snoRNA寻找可能的指导位点表明，与内含子相比，这些分子的另一个亚组（HBII-85）具有统计学上升高的对外显子的指导偏好。此外，HBII-85 snoRNA的这些能量上有利的推定靶点与产生选择性剪接mRNA同种型的基因非随机相关。snoTARGET资源可在http://hsc.utoledo.edu/depts/bioinfo/snotarget.html上免费获得。(c)2007 Elsevier B. V.保留所有权利。
Among thousands of non-protein-coding RNAs which have been found in humans, a significant group represents snoRNA molecules that guide other types of RNAs to specific chemical modifications, cleavages, or proper folding. Yet, hundreds of mammalian snoRNAs have unknown function and are referred to as "orphan" molecules. In 2006, for the first time, it was shown that a particular orphan snoRNA (HBII-52) plays an important role in the regulation of alternative splicing of the serotonin receptor gene in humans and other mammals. In order to facilitate the investigation of possible involvement of snoRNAs in the regulation of pre-mRNA processing, we developed a new computational web resource, snoTARGET, which searches for possible guiding sites for snoRNAs among the entire set of human and rodent exonic and intronic sequences. Application of snoTARGET for finding possible guiding sites for a number of human and rodent orphan C/D-box snoRNAs showed that another subgroup of these molecules (HBII-85) have statistically elevated guiding preferences toward exons compared to introns. Moreover, these energetically favorable putative targets of HBII-85 snoRNAs are non-randomly associated with genes producing alternatively spliced mRNA isoforms. The snoTARGET resource is freely available at http://hsc.utoledo.edu/depts/bioinfo/snotarget.html. (c) 2007 Elsevier B.V. All rights reserved.