Department of Microbiology & Molecular Genetics, University of California, Irvine, Irvine, CA 92697-4025, USA.
Nucleic Acids Res. 2011 Nov 1;39(20):8928-37. doi: 10.1093/nar/gkr481. Epub 2011 Jul 27.
Pre-mRNA splicing is carried out by the spliceosome, which identifies exons and removes intervening introns. In vertebrates, most splice sites are initially recognized by the spliceosome across the exon, because most exons are small and surrounded by large introns. This gene architecture predicts that efficient exon recognition depends largely on the strength of the flanking 3' and 5' splice sites. However, it is unknown if the 3' or the 5' splice site dominates the exon recognition process. Here, we test the 3' and 5' splice site contributions towards efficient exon recognition by systematically replacing the splice sites of an internal exon with sequences of different splice site strengths. We show that the presence of an optimal splice site does not guarantee exon inclusion and that the best predictor for exon recognition is the sum of both splice site scores. Using a genome-wide approach, we demonstrate that the combined 3' and 5' splice site strengths of internal exons provide a much more significant separator between constitutive and alternative exons than either the 3' or the 5' splice site strength alone.
前体 mRNA 的剪接是由剪接体完成的，剪接体识别外显子并去除中间的内含子。在脊椎动物中，大多数剪接位点最初是由剪接体在exon 两侧识别的，因为大多数 exon 很小，周围是较大的内含子。这种基因结构预测，有效的exon 识别在很大程度上取决于侧翼 3' 和 5' 剪接位点的强度。然而，目前还不清楚是 3' 剪接位点还是 5' 剪接位点在 exon 识别过程中起主导作用。在这里，我们通过系统地用不同剪接位点强度的序列替换内部 exon 的剪接位点，来测试 3' 和 5' 剪接位点对有效 exon 识别的贡献。我们表明，存在最优剪接位点并不能保证 exon 的包含，exon 识别的最佳预测因子是两个剪接位点得分的总和。我们使用全基因组方法表明，内部 exon 的组合 3' 和 5' 剪接位点强度比单独的 3' 或 5' 剪接位点强度更能显著地区分组成型和选择性 exon。
