Despite a growing number of splicing mutations found in hereditary diseases, utilization of aberrant splice sites and their effects on gene expression remain challenging to predict. We compiled sequences of 346 aberrant 5'splice sites (5'ss) that were activated by mutations in 166 human disease genes. Mutations within the 5'ss consensus accounted for 254 cryptic 5'ss and mutations elsewhere activated 92 de novo 5'ss. Point mutations leading to cryptic 5'ss activation were most common in the first intron nucleotide, followed by the fifth nucleotide. Substitutions at position +5 were exclusively G>A transitions, which was largely attributable to high mutability rates of C/G>T/A. However, the frequency of point mutations at position +5 was significantly higher than that observed in the Human Gene Mutation Database, suggesting that alterations of this position are particularly prone to aberrant splicing, possibly due to a requirement for sequential interactions with U1 and U6 snRNAs. Cryptic 5'ss were best predicted by computational algorithms that accommodate nucleotide dependencies and not by weight-matrix models. Discrimination of intronic 5'ss from their authentic counterparts was less effective than for exonic sites, as the former were intrinsically stronger than the latter. Computational prediction of exonic de novo 5'ss was poor, suggesting that their activation critically depends on exonic splicing enhancers or silencers. The authentic counterparts of aberrant 5'ss were significantly weaker than the average human 5'ss. The development of an online database of aberrant 5'ss will be useful for studying basic mechanisms of splice-site selection, identifying splicing mutations and optimizing splice-site prediction algorithms.

译文

尽管遗传性疾病中发现了越来越多的剪接突变,但异常剪接位点的利用及其对基因表达的影响仍难以预测。我们汇编了346个异常5' 剪接位点 (5'ss) 的序列,这些位点被166人类疾病基因的突变激活。5'ss共识内的突变占254个隐秘的5'ss,而其他地方的突变从头激活92个5'ss。导致隐式5'ss激活的点突变最常见于第一个内含子核苷酸,其次是第五个核苷酸。位置5的取代仅是G>A跃迁,这在很大程度上归因于C/G>T/A的高变异性。然而,5位点突变的频率明显高于人类基因突变数据库中观察到的频率,这表明该位置的改变特别容易产生异常剪接,这可能是由于需要与U1和U6 snrna的顺序相互作用。最好通过适应核苷酸依赖性的计算算法而不是通过权重矩阵模型来预测隐式5'ss。将内含子5'ss与真实的对应物区分的效果不如外显子位点,因为前者本质上比后者强。外显子从头5'ss的计算预测很差,表明它们的激活主要取决于外显子剪接增强剂或消音器。异常5'ss的真实对应物明显弱于人类的平均5'ss。异常5'ss在线数据库的开发将有助于研究剪接位点选择的基本机制,识别剪接突变和优化剪接位点预测算法。

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