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Cell Rep. 2019 Jul 30;28(5):1219-1236.e11. doi: 10.1016/j.celrep.2019.06.088.

The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila.

Author information

1
European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Electronic address: obrdlik@embl.de.
2
European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
3
Department for Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK.
4
Department for Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK; The Francis Crick Institute, London NW1 1AT, UK.
5
European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Electronic address: ephrussi@embl.de.

Abstract

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.

KEYWORDS:

DSP crosslinking; Drosophila EJC; EJC assembly regulation; EJC-ipaRt; cytoplasm; exon junction complex; ipaRt; organismal interactome

PMID:
31365866
DOI:
10.1016/j.celrep.2019.06.088
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