Identification of common genetic variation that modulates alternative splicing
Identification of common genetic variation that modulates alternative splicing
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DOI：
10.1371/journal.pgen.0030099
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发表时间：
2007-06-01
期刊：
影响因子：
4.5
通讯作者：
Kwiatkowski, Dominic
中科院分区：
文献类型：
--
作者：
Hull, Jeremy;Campino, Susana;Kwiatkowski, Dominic
基因的可变剪接是产生蛋白质功能变异的一种有效手段。一些疾病状态与影响剪接模式的罕见遗传变异有关。相反，已知一些基因的剪接效率在个体之间存在差异，但没有明显的不良影响。目前尚不清楚的是，通常观察到的剪接模式的表型变异，以及因此可能产生的蛋白质功能变异，在很大程度上是否由自然发生的DNA序列变异决定，特别是由单核苷酸多态性（SNPs）决定。在这项研究中，我们调查了22名先前由国际人类基因组单体型图计划（International HapMap Project）进行基因分型的个体中250个外显子的剪接模式。我们在我们的实验系统中确定了70个简单的盒式外显子可变剪接事件；对于其中6个事件，我们检测到个体之间剪接模式存在一致的差异，并且剪接表型与邻近的SNPs之间具有高度显著的关联。值得注意的是，对于其中6个事件中的5个，与最接近内含子 - 外显子边界的SNP相关性最强，尽管这些SNPs与内含子 - 外显子边界之间的距离从2个碱基对到大于1000个碱基对不等。使用小基因剪接系统对其中两个SNPs进行了进一步研究，在每种情况下，都发现这些SNPs在体外对外显子剪接效率具有顺式作用。使用生物信息学算法无法预测这些SNPs的功能后果。我们的研究结果表明，剪接模式的表型变异是由侧翼内含子或外显子内SNPs的存在决定的。对剪接的影响可能是SNPs影响基因功能的一种重要机制。
Alternative splicing of genes is an efficient means of generating variation in protein function. Several disease states have been associated with rare genetic variants that affect splicing patterns. Conversely, splicing efficiency of some genes is known to vary between individuals without apparent ill effects. What is not clear is whether commonly observed phenotypic variation in splicing patterns, and hence potential variation in protein function, is to a significant extent determined by naturally occurring DNA sequence variation and in particular by single nucleotide polymorphisms (SNPs). In this study, we surveyed the splicing patterns of 250 exons in 22 individuals who had been previously genotyped by the International HapMap Project. We identified 70 simple cassette exon alternative splicing events in our experimental system; for six of these, we detected consistent differences in splicing pattern between individuals, with a highly significant association between splice phenotype and neighbouring SNPs. Remarkably, for five out of six of these events, the strongest correlation was found with the SNP closest to the intron exon boundary, although the distance between these SNPs and the intron-exon boundary ranged from 2 bp to greater than 1,000 bp. Two of these SNPs were further investigated using a minigene splicing system, and in each case the SNPs were found to exert cis-acting effects on exon splicing efficiency in vitro. The functional consequences of these SNPs could not be predicted using bioinformatic algorithms. Our findings suggest that phenotypic variation in splicing patterns is determined by the presence of SNPs within flanking introns or exons. Effects on splicing may represent an important mechanism by which SNPs influence gene function.