Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel.
Nucleic Acids Res. 2010 Jun;38(10):3318-27. doi: 10.1093/nar/gkq005. Epub 2010 Jan 27.
Regulation of splicing in eukaryotes occurs through the coordinated action of multiple splicing factors. Exons and introns contain numerous putative binding sites for splicing regulatory proteins. Regulation of splicing is presumably achieved by the combinatorial output of the binding of splicing factors to the corresponding binding sites. Although putative regulatory sites often overlap, no extensive study has examined whether overlapping regulatory sequences provide yet another dimension to splicing regulation. Here we analyzed experimentally-identified splicing regulatory sequences using a computational method based on the natural distribution of nucleotides and splicing regulatory sequences. We uncovered positive and negative interplay between overlapping regulatory sequences. Examination of these overlapping motifs revealed a unique spatial distribution, especially near splice donor sites of exons with weak splice donor sites. The positively selected overlapping splicing regulatory motifs were highly conserved among different species, implying functionality. Overall, these results suggest that overlap of two splicing regulatory binding sites is an evolutionary conserved widespread mechanism of splicing regulation. Finally, over-abundant motif overlaps were experimentally tested in a reporting minigene revealing that overlaps may facilitate a mode of splicing that did not occur in the presence of only one of the two regulatory sequences that comprise it.
真核生物中的剪接调控是通过多种剪接因子的协调作用来实现的。外显子和内含子包含许多推测的剪接调控蛋白结合位点。剪接的调控可能是通过剪接因子与相应结合位点的结合的组合输出来实现的。尽管推测的调控位点经常重叠，但没有广泛的研究来检验重叠的调控序列是否为剪接调控提供了另一个维度。在这里，我们使用基于核苷酸和剪接调控序列自然分布的计算方法，对实验鉴定的剪接调控序列进行了分析。我们揭示了重叠调控序列之间的正、负相互作用。对这些重叠基序的检查揭示了一种独特的空间分布，特别是在弱供体位点的外显子的供体位点附近。在不同物种中，这些被选择的重叠剪接调控基序高度保守，暗示了其功能。总的来说，这些结果表明，两个剪接调控结合位点的重叠是剪接调控的一种广泛存在的进化保守机制。最后，在一个报告基因的实验中，对过度丰富的基序重叠进行了测试，结果表明重叠可能促进了一种剪接模式，而这种模式在只有两个组成调控序列之一的情况下不会发生。
