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| Status |
Public on Jul 30, 2019 |
| Title |
Role of the Exon Junction Complex in Danio rerio |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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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| |
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| Overall design |
Analysis of exon junction complex (EJC) footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants
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| |
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| Contributor(s) |
Singh G, Gangras P |
| Citation |
*P. Gangras*, T. Gallagher, R. Patton, Z.Yi, M. Parthun, K. Tietz, N. Deans, R. Bundschuh, S. Amacher, G. Singh (2019); Stop codon proximal 3'UTR introns in vertebrates can elicit EJC-dependent nonsense-mediated mRNA decay. (Preprint on BioRxiv doi: https://0-doi-org.brum.beds.ac.uk/10.1101/677666)
|
| Submission date |
Jul 29, 2019 |
| Last update date |
Oct 29, 2019 |
| Contact name |
Pooja Gangras |
| E-mail(s) |
poojagangras23@gmail.com
|
| Phone |
6149060940
|
| Organization name |
The Ohio State University
|
| Department |
Molecular Genetics
|
| Lab |
Guramrit Singh
|
| Street address |
191 W. 9th Ave, apt A3
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43201 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
| GPL18413 |
Illumina HiSeq 2500 (Danio rerio) |
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| Samples (26)
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| Relations |
| BioProject |
PRJNA557179 |
| SRA |
SRP216689 |
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