European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Cell Rep. 2019 Jul 30;28(5):1219-1236.e11. doi: 10.1016/j.celrep.2019.06.088.
Exon junction complex (EJC) assembles after splicing at specific positions upstream of exon-exon junctions in mRNAs of all higher eukaryotes, affecting major regulatory events. In mammalian cell cytoplasm, EJC is essential for efficient RNA surveillance, while in Drosophila, EJC is essential for localization of oskar mRNA. Here we developed a method for isolation of protein complexes and associated RNA targets (ipaRt) to explore the EJC RNA-binding landscape in a transcriptome-wide manner in adult Drosophila. We find the EJC at canonical positions, preferably on mRNAs from genes comprising multiple splice sites and long introns. Moreover, EJC occupancy is highest at junctions adjacent to strong splice sites, CG-rich hexamers, and RNA structures. Highly occupied mRNAs tend to be maternally localized and derive from genes involved in differentiation or development. These modalities, which have not been reported in mammals, specify EJC assembly on a biologically coherent set of transcripts in Drosophila.
外显子连接复合体 (EJC) 在所有高等真核生物的 mRNA 中外显子-外显子交界处的上游特定位置拼接后组装，影响主要的调控事件。在哺乳动物细胞质中，EJC 对于有效的 RNA 监测至关重要，而在果蝇中，EJC 对于 Oskar mRNA 的定位至关重要。在这里，我们开发了一种用于分离蛋白质复合物和相关 RNA 靶标的方法（ipaRt），以在成年果蝇中以全转录组的方式探索 EJC 的 RNA 结合图谱。我们发现 EJC 位于典型位置，最好是在包含多个剪接位点和长内含子的基因的 mRNA 上。此外，EJC 占据率在靠近强剪接位点、富含 CG 的六聚体和 RNA 结构的交界处最高。高度占据的 mRNA 往往是母系定位的，并且来自参与分化或发育的基因。这些模式在哺乳动物中尚未报道，指定了果蝇中一组具有生物学一致性的 EJC 组装转录本。
