Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA330543 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3931861.fastq.gz | Fastqsanger.gz | |||
| SRR3931862.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
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Project description:The exon junction complex (EJC) is composed of three core proteins Rbm8a, Magoh and Eif4a3 and is thought to play a role in several post-transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome-wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing (RIP-Seq). We find that, as in human cells, zebrafish EJC is deposited about 24 nts upstream of exon-exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA-seq from rbm8a mutant, magoh mutant and wild-type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants.
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Project description:To uncover exon junction complex (EJC) deposition sites on cellular mRNAs, RNA footprints of EJC immuo-purified from HEK293 cells were deep sequenced. The analysis of these data revealed that major “canonical” EJC occupancy site in vivo lies 24 nucleotides upstream of exon junctions (-24 position) and that the majority of exon junctions carry an EJC. Unexpectedly, we find that many sites further upstream of -24 position are also enriched in these EJC footprints. These "non-canonical" sites are binding sites of EJC-interacting proteins with a subset being occupied by SR proteins. Thus, an EJC-SR protein nexus exists within spliced mRNPs and is revealed here.
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Project description:During pre-mRNA splicing in the nucleus, the spliceosome deposits the Exon Junction Complex (EJC) ~24 nucleotides upstream of exon-exon junctions. The EJC core thus deposited comprises of EIF4A3, RBM8A and MAGOH and remains stably bound to RNA to modulate mRNA fate at multiple post-transcriptional steps until its disassembly during translation. Such EJC disassembly is proposed to be mediated by PYM1, a factor that can bind both the ribosome and the RBM8A/MAGOH heterodimer of the EJC core. Here, we investigated the role of PYM1 in regulating EJC binding in human embryonic kidney 293 (HEK293) cells using a MAGOH mutant that assembles into EJC but is impaired in PYM1 interaction. We find that EJCs lacking PYM1 interaction show no defect in translation dependent disassembly. Surprisingly, PYM1 interaction deficient EJCs are enriched on sites away from the canonical EJC binding position including on transcripts without introns or fewer and longer exons. Additionally, acute reduction and elevation of PYM1 levels in HEK293 cells result in a modest NMD inhibition and stabilization of mRNAs that localize to endoplasmic reticulum associated TIS-granules and are characterized by fewer and longer exons. These gene expression changes are mirrored in flavivirus infected cells, suggesting a potential role for PYM1 in host-pathogen interactions, as flaviviruses are known to target this protein.
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Project description:Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans. Here we find that the nuclear exon junction complex (pre-EJC) is a critical and conserved regulator of this process. Depletion of pre-EJC subunits leads to a global decrease in Pol II pausing and to premature entry into elongation. This effect occurs, at least in part, via non-canonical recruitment of pre-EJC components at promoters. Failure to recruit the pre-EJC at promoters results in increased binding of the positive transcription elongation complex (P-TEFb) and in enhanced Pol II release. Notably, restoring pausing is sufficient to rescue exon skipping and the photoreceptor differentiation defect associated with depletion of pre-EJC components in vivo. We propose that the pre-EJC serves as an early transcriptional checkpoint to prevent premature entry into elongation, ensuring proper recruitment of RNA processing components that are necessary for exon definition.
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