10779/crick.11559813.v1 Ales Obrdlik Ales Obrdlik Gen Lin Gen Lin Nejc Haberman Nejc Haberman Jernej Ule Jernej Ule Anne Ephrussi Anne Ephrussi The transcriptome-wide landscape and modalities of EJC binding in adult Drosophila. The Francis Crick Institute 2020 DSP crosslinking Drosophila EJC EJC assembly regulation EJC-ipaRt cytoplasm exon junction complex ipaRt organismal interactome Ule - sec 0601 Biochemistry and Cell Biology 2020-01-09 16:44:58 Journal contribution https://crick.figshare.com/articles/journal_contribution/The_transcriptome-wide_landscape_and_modalities_of_EJC_binding_in_adult_Drosophila_/11559813 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.