Brendel V, Kleffe J, Carle-Urioste J C, Walbot V
Department of Mathematics, Stanford University, CA 94305-2125, USA.
J Mol Biol. 1998 Feb 13;276(1):85-104. doi: 10.1006/jmbi.1997.1523.
Heterologous introns are often inaccurately or inefficiently processed in higher plants. The precise features that distinguish the process of pre-mRNA splicing in plants from splicing in yeast and mammals are unclear. One contributing factor is the prominent base compositional contrast between U-rich plant introns and flanking G + C-rich exons. Inclusion of this contrast factor in recently developed statistical methods for splice site prediction from sequence inspection significantly improved prediction accuracy. We applied the prediction tools to re-analyze experimental data on splice site selection and splicing efficiency for native and more than 170 mutated plant introns. In almost all cases, the experimentally determined preferred sites correspond to the highest scoring sites predicted by the model. In native genes, about 90% of splice sites are the locally highest scoring sites within the bounds of the flanking exon and intron. We propose that, in most cases, local context (about 50 bases upstream and downstream from a potential intron end) is sufficient to account for intrinsic splice site strength, and that competition for transacting factors determines splice site selection in vivo. We suggest that computer-aided splice site prediction can be a powerful tool for experimental design and interpretation.
异源内含子在高等植物中常常被不准确或低效地加工。目前尚不清楚将植物前体mRNA剪接过程与酵母和哺乳动物剪接过程区分开来的确切特征。一个促成因素是富含U的植物内含子与侧翼富含G + C的外显子之间显著的碱基组成差异。将这种差异因素纳入最近开发的用于通过序列检查预测剪接位点的统计方法中，显著提高了预测准确性。我们应用这些预测工具重新分析了关于天然及170多个突变植物内含子的剪接位点选择和剪接效率的实验数据。在几乎所有情况下，实验确定的首选位点都与模型预测的得分最高的位点相对应。在天然基因中，约90%的剪接位点是侧翼外显子和内含子范围内局部得分最高的位点。我们提出，在大多数情况下，局部上下文（潜在内含子末端上下游约50个碱基）足以解释内在剪接位点强度，并且对反式作用因子的竞争决定了体内剪接位点的选择。我们认为计算机辅助的剪接位点预测可以成为实验设计和解释的有力工具。
