Systematic Evaluation of the Effect of Common SNPs on Pre-mRNA Splicing
Systematic Evaluation of the Effect of Common SNPs on Pre-mRNA Splicing
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DOI：
10.1002/humu.20906
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发表时间：
2009-04-01
期刊：
影响因子：
3.9
通讯作者：
Hampe, Jochen
中科院分区：
文献类型：
--
作者：
ElSharawy, Abdou;Hundrieser, Bernd;Hampe, Jochen
差异信使核糖核酸剪接在进化和生物医学上的重要性已得到充分证实。许多研究已经评估了不同基因的差异剪接模式，并将这些模式与相邻的单核苷酸多态(SNPs)的基因类型相关联。在这里，我们选择了一种相反的方法，并在典型剪接位点或外显子剪接增强子(ESES)上筛选常见的SNP，这些外显子剪接增强子将被生物信息学工具归类为假定剪接相关。使用先前建立的由92个匹配DNA和cDNA组成的小组对从数据库SNP检索到的223个候选SNP进行了实验测试。对于每个SNP，通过巢式RT-PCR和随后的测序，研究了16个在各自SNP上提供平衡的基因类型的cDNA。通过对扩增产物的克隆，验证了可能的等位基因、依赖剪接。生物信息学工具的阳性预测值很低，从ESEfinder的0%到最近报道的神经网络的99%(在受体位点SNP的情况下)不等。这些结果突显了需要更好地了解功能剪接位点的序列特征，以提高我们在计算机中预测经验观察到的DNA序列变体的剪接相关性的能力。2009年，Hum Mutat 30,625-632。(C)2009年Wiley-Liss，Inc.
The evolutionary and biomedical importance of differential mRNA splicing is well established. Numerous studies have assessed patterns of differential splicing in different genes and correlated these patterns to the genotypes for adjacent single,nucleotide polymorphisms (SNPs). Here, We have chosen a reverse approach and screened dbSNP for common SNPs at either canonical splice sites or exonic splice enhancers (ESEs) that would be classified as putatively splicing-relevant by bioinformatic tools. The 223 candidate SNPs retrieved from dbSNP were experimentally tested using a previously established panel of 92 matching DNAs and cDNAs. For each SNP, 16 cDNAs providing a balanced representation of the genotypes at the respective SNP were investigated by nested RT-PCR and subsequent sequencing. Putative allele,dependent splicing was verified by the cloning of PCR products. The positive predictive value of the bioinformatics tools turned out to be low,, ranging from 0% for ESEfinder to 99% (in the case of acceptor-site SNPs) for a recently reported neural network. The results highlight the need for a better understanding of the sequence characteristics of functional splice-sites to improve our ability to predict in silico the splicing relevance of empirically observed DNA sequence variants. Hum Mutat 30, 625-632, 2009. (C) 2009 Wiley-Liss, Inc.