Differential connectivity of splicing activators and repressors to the human spliceosome.
Differential connectivity of splicing activators and repressors to the human spliceosome.
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DOI：
10.1186/s13059-015-0682-5
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发表时间：
2015-06-06
期刊：
影响因子：
12.3
通讯作者：
Krainer AR
中科院分区：
文献类型：
--
作者：
Akerman M;Fregoso OI;Das S;Ruse C;Jensen MA;Pappin DJ;Zhang MQ;Krainer AR
在剪接体组装过程中，蛋白质-蛋白质相互作用（PPI）依次形成和破坏，以适应前体mRNA底物识别和催化的空间要求。剪接激活因子和抑制因子（例如SR蛋白和hnRNP）调节剪接体组装并调节选择性剪接。然而，目前尚不清楚它们如何与核心剪接体差异相互作用以执行其功能。在这里，我们调查的SR和hnRNP蛋白质的核心剪接体的蛋白质连接使用概率网络重建的基础上整合的相互作用和基因表达数据。我们通过免疫沉淀和质谱分析原型剪接因子SRSF 1和hnRNPA 1来验证我们的模型。网络分析表明，一个因子作为激活子或阻遏子的特性可以从其与剪接体其余部分的整体连接性来预测。此外，我们发现并实验验证了癌蛋白SRSF 1和抗肿瘤药物靶点SF 3复合物成员之间的PPI。我们的研究结果表明，激活剂促进剪接体亚复合物之间PPI的形成，而阻遏物主要通过蛋白质-RNA相互作用。这项研究表明，将计算机模拟与生物化学相结合可以显着提高对人类剪接体结构和功能关系的理解。本文的在线版本（doi：10.1186/s13059-015-0682-5）包含补充材料，可供授权用户使用。
During spliceosome assembly, protein-protein interactions (PPI) are sequentially formed and disrupted to accommodate the spatial requirements of pre-mRNA substrate recognition and catalysis. Splicing activators and repressors, such as SR proteins and hnRNPs, modulate spliceosome assembly and regulate alternative splicing. However, it remains unclear how they differentially interact with the core spliceosome to perform their functions. Here, we investigate the protein connectivity of SR and hnRNP proteins to the core spliceosome using probabilistic network reconstruction based on the integration of interactome and gene expression data. We validate our model by immunoprecipitation and mass spectrometry of the prototypical splicing factors SRSF1 and hnRNPA1. Network analysis reveals that a factor’s properties as an activator or repressor can be predicted from its overall connectivity to the rest of the spliceosome. In addition, we discover and experimentally validate PPIs between the oncoprotein SRSF1 and members of the anti-tumor drug target SF3 complex. Our findings suggest that activators promote the formation of PPIs between spliceosomal sub-complexes, whereas repressors mostly operate through protein-RNA interactions. This study demonstrates that combining in-silico modeling with biochemistry can significantly advance the understanding of structure and function relationships in the human spliceosome. The online version of this article (doi:10.1186/s13059-015-0682-5) contains supplementary material, which is available to authorized users.