Danks et al. 2019 (PRJNA474431)
General Details
| Title | Genome-wide profiling of translation in Oikopleura dioica during growth arrest and recovery |
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| Organism | |
| Number of Samples | 8 |
| Release Date | 2018/06/04 00:00 |
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| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP149663 |
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| ENA | SRP149663 |
| GEO | |
| BioProject | PRJNA474431 |
Publication
| Title | |
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| Authors | Danks GB,Galbiati H,Raasholm M,Torres Cleuren YN,Valen E,Navratilova P,Thompson EM |
| Journal | BMC genomics |
| Publication Date | 2019 Nov 29 |
| Abstract | In phylogenetically diverse organisms, the 5' ends of a subset of mRNAs are trans-spliced with a spliced leader (SL) RNA. The functions of SL trans-splicing, however, remain largely enigmatic. We quantified translation genome-wide in the marine chordate, Oikopleura dioica, under inhibition of mTOR, a central growth regulator. Translation of trans-spliced TOP mRNAs was suppressed, consistent with a role of the SL sequence in nutrient-dependent translational control of growth-related mRNAs. Under crowded, nutrient-limiting conditions, O. dioica continued to filter-feed, but arrested growth until favorable conditions returned. Upon release from unfavorable conditions, initial recovery was independent of nutrient-responsive, trans-spliced genes, suggesting animal density sensing as a first trigger for resumption of development. Our results are consistent with a proposed role of trans-splicing in the coordinated translational down-regulation of nutrient-responsive genes under growth-limiting conditions. |
| PMC | PMC6883708 |
| PMID | 31783727 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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| SRR7252574 | PRJNA474431 | Oikopleura dioica | Ribo-Seq |  |
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| SRR7252575 | PRJNA474431 | Oikopleura dioica | Ribo-Seq | |
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| SRR7252576 | PRJNA474431 | Oikopleura dioica | Ribo-Seq | |
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| SRR7252577 | PRJNA474431 | Oikopleura dioica | Ribo-Seq | |
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| SRR7252578 | PRJNA474431 | Oikopleura dioica | RNA-Seq | |
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| SRR7252579 | PRJNA474431 | Oikopleura dioica | RNA-Seq | |
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| SRR7252580 | PRJNA474431 | Oikopleura dioica | RNA-Seq | |
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| SRR7252581 | PRJNA474431 | Oikopleura dioica | RNA-Seq | |
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| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
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