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

Obrdlik, A; Lin, G; Haberman, N; Ule, J; Ephrussi, A; (2019) The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila. Cell Reports , 28 (5) 1219-1236.e11. 10.1016/j.celrep.2019.06.088. Green open access

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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.

Type: Article
Title: The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.celrep.2019.06.088
Publisher version: https://doi.org/10.1016/j.celrep.2019.06.088
Language: English
Additional information: © 2019 The Author(s). This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Keywords: DSP crosslinking, Drosophila EJC, EJC assembly regulation, EJC-ipaRt, cytoplasm, exon junction complex, ipaRt, organismal interactome
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Department of Neuromuscular Diseases
URI: https://discovery.ucl.ac.uk/id/eprint/10079368
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