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Transcriptome-wide binding sites of mutually exclusive exon junction complexes

ABSTRACT: The exon junction complex (EJC) deposited upstream of mRNA exon junctions shapes structure, composition and fate of spliced mRNA ribonucleoprotein particles (mRNPs). To achieve this, the EJC core nucleates assembly of a dynamic shell of peripheral proteins that function in diverse post-transcriptional processes. In this study we show that EJC exists in two mutually exclusive compositions characterized by peripheral proteins RNPS1 and CASC3. We identified transcriptome-wide binding sites of the two alternate EJCs via RNA:protein immunoprecipitation in tandem followed by deep sequencing (RIPiT-Seq). We show that RNPS1-EJC, which is an SR-rich mega-dalton sized RNP, is the major EJC form in the nucleus. After mRNP export to the cytoplasm and before translation, the EJC undergoes a remarkable compositional and structural remodeling into an SR- and RNPS1-devoid monomeric complex that contains CASC3. The CASC3-EJC is enriched on cytoplasmic RNAs and is the main EJC form that encounters ribosome and undergoes disassembly during translation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE115977 | GEO | 2018/11/19

REPOSITORIES: GEO

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Insights into transcriptome surveillance and alternative splicing regulation by the EJC-associated splicing factor RNPS1

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2022-05-31 | PXD027251 | Pride

The exon junction complex controls transposable element activity by ensuring the faithful splicing of the piwi transcript

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2014-09-08 | E-GEOD-57710 | biostudies-arrayexpress

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Genome-wide identification of circRNAs translated by eIF4A3

Project description:Exon junction complexes (EJCs) deposited on spliced mRNAs play multifunctional roles in the regulation of gene expression. Whereas the formation and components of EJCs are well characterized, the underlying molecular mechanisms for gene regulation remain poorly understood. Here we find that a eukaryotic translation initiation factor (eIF) 4A3, a core component of EJC directly interacts with eIF3g, a subunit of eIF3 complex. This interaction serves as a linker between the EJC and eIF3 complex, consequently driving an internal ribosomal recruitment. Accordingly, artificially tethered EJC component or cellular EJC deposited on mRNA after splicing promotes internal initiation of translation in a way that is resistant to cellular stress induced by serum starvation. We also demonstrate that translatable endogenous or reporter circular RNAs depend on EJC for their association with polysomes. Our results uncover an internal initiation driven by EJC, expanding the protein-coding potential of human transcriptome including circular RNAs.

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2014-11-04 | E-GEOD-33475 | biostudies-arrayexpress

The exon junction complex controls transposable element activity by ensuring the faithful splicing of the piwi transcript

2014-09-08 | GSE57710 | GEO

The exon junction complex is restricted to a specific subset of splice junctions

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Project description:Splicing of pre-mRNAs results in the deposition of the exon junction complex (EJC) upstream of exon-exon boundaries. The EJC plays crucial post-splicing roles in export, translation, localization and nonsense-mediated decay of mRNAs. It also aids faithful splicing of pre-mRNAs containing large introns, albeit via an unknown mechanism. Here, we show that the core EJC plus the accessory factors RnpS1 and Acinus aid in definition and efficient splicing of neighboring introns. This requires prior deposition of the EJC in close proximity either from an upstream or downstream splicing event. If present in isolation, EJC-dependent introns are splicing-defective also in wildtype cells. Interestingly, the most affected intron belongs to the piwi locus, which explains the reported transposon de-silencing in EJC-depleted Drosophila ovaries. We propose that the dependency of splicing on the EJC is exploited as a means to control the temporal order of splicing events. Our observations provide a powerful basis to dissect the molecular events that underlie the role of the EJC in splicing.

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