The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila
Summary: 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 essentia...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2019-07-01
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| Series: | Cell Reports |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S221112471930868X |
| _version_ | 1811282908161245184 |
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| author | Ales Obrdlik Gen Lin Nejc Haberman Jernej Ule Anne Ephrussi |
| author_facet | Ales Obrdlik Gen Lin Nejc Haberman Jernej Ule Anne Ephrussi |
| author_sort | Ales Obrdlik |
| collection | DOAJ |
| description | Summary: 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. : Obrdlik et al. present ipaRt, an approach for definition of the EJC-RNA-binding landscape in adult Drosophila melanogaster. Their study uncovers the impact of gene architecture, splice site strength, RNA structures, and CUG hexamers on EJC binding and provides insights into the evolution of EJC functions. Keywords: exon junction complex, Drosophila EJC, ipaRt, organismal interactome, DSP crosslinking, EJC-ipaRt, cytoplasm, EJC assembly regulation |
| first_indexed | 2024-04-13T02:00:58Z |
| format | Article |
| id | doaj.art-cb5fd0009d9d456180c3ee1873d1c07b |
| institution | Directory Open Access Journal |
| issn | 2211-1247 |
| language | English |
| last_indexed | 2024-04-13T02:00:58Z |
| publishDate | 2019-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj.art-cb5fd0009d9d456180c3ee1873d1c07b2022-12-22T03:07:38ZengElsevierCell Reports2211-12472019-07-0128512191236.e11The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult DrosophilaAles Obrdlik0Gen Lin1Nejc Haberman2Jernej Ule3Anne Ephrussi4European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Corresponding authorEuropean Molecular Biology Laboratory, 69117 Heidelberg, GermanyDepartment for Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UKDepartment for Neuromuscular Diseases, UCL Institute of Neurology, London WC1N 3BG, UK; The Francis Crick Institute, London NW1 1AT, UKEuropean Molecular Biology Laboratory, 69117 Heidelberg, Germany; Corresponding authorSummary: 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. : Obrdlik et al. present ipaRt, an approach for definition of the EJC-RNA-binding landscape in adult Drosophila melanogaster. Their study uncovers the impact of gene architecture, splice site strength, RNA structures, and CUG hexamers on EJC binding and provides insights into the evolution of EJC functions. Keywords: exon junction complex, Drosophila EJC, ipaRt, organismal interactome, DSP crosslinking, EJC-ipaRt, cytoplasm, EJC assembly regulationhttp://www.sciencedirect.com/science/article/pii/S221112471930868X |
| spellingShingle | Ales Obrdlik Gen Lin Nejc Haberman Jernej Ule Anne Ephrussi The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila Cell Reports |
| title | The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila |
| title_full | The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila |
| title_fullStr | The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila |
| title_full_unstemmed | The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila |
| title_short | The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila |
| title_sort | transcriptome wide landscape and modalities of ejc binding in adult drosophila |
| url | http://www.sciencedirect.com/science/article/pii/S221112471930868X |
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