Bazeley Peter S, Shepelev Valery, Talebizadeh Zohreh, Butler Merlin G, Fedorova Larisa, Filatov Vadim, Fedorov Alexei
Program in Bioinformatics and Proteomics/Genomics, University of Toledo Health Science Campus, Toledo, OH 43614, USA.
Gene. 2008 Jan 31;408(1-2):172-9. doi: 10.1016/j.gene.2007.10.037. Epub 2007 Nov 21.
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).
在人类中发现的数千种非蛋白质编码RNA中，有一组重要的是snoRNA分子，它们引导其他类型的RNA进行特定的化学修饰、切割或正确折叠。然而，数百种哺乳动物snoRNA的功能尚不清楚，被称为“孤儿”分子。2006年，首次发现一种特定的孤儿snoRNA（HBII-52）在人类和其他哺乳动物中对血清素受体基因的可变剪接调控中起重要作用。为了便于研究snoRNA可能参与前体mRNA加工调控的情况，我们开发了一种新的计算网络资源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的可能引导位点。应用snoTARGET寻找多种人类和啮齿动物孤儿C/D盒snoRNA的可能引导位点表明，与内含子相比，这些分子的另一个亚组（HBII-85）对外显子的引导偏好具有统计学上的升高。此外，HBII-85 snoRNA的这些能量有利的推定靶标与产生可变剪接mRNA异构体的基因非随机相关。snoTARGET资源可在以下网址免费获取：(http://hsc.utoledo.edu/depts/bioinfo/snotarget.html)。
