Han et al. 2020 (PRJNA590355)
General Details
| Title | Genome-wide survey of ribosome collision [anisomycin] |
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| Organism | |
| Number of Samples | 2 |
| Release Date | 2019/11/19 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP230602 |
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| ENA | SRP230602 |
| GEO | GSE140639 |
| BioProject | PRJNA590355 |
Publication
| Title | |
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| Authors | Han P, Shichino Y, Schneider-Poetsch T, Mito M, Hashimoto S, Udagawa T, Kohno K, Yoshida M, Mishima Y, Inada T, Iwasaki S |
| Journal | Cell reports |
| Publication Date | 2020 May 5 |
| Abstract | Ribosome movement is not always smooth and is rather often impeded. For ribosome pauses, fundamental issues remain to be addressed, including where ribosomes pause on mRNAs, what kind of RNA/amino acid sequence causes this pause, and the physiological significance of this attenuation of protein synthesis. Here, we survey the positions of ribosome collisions caused by ribosome pauses in humans and zebrafish using modified ribosome profiling. Collided ribosomes, i.e., disomes, emerge at various sites: Pro-Pro/Gly/Asp motifs; Arg-X-Lys motifs; stop codons; and 3' untranslated regions. The electrostatic interaction between the charged nascent chain and the ribosome exit tunnel determines the eIF5A-mediated disome rescue at the Pro-Pro sites. In particular, XBP1u, a precursor of endoplasmic reticulum (ER)-stress-responsive transcription factor, shows striking queues of collided ribosomes and thus acts as a degradation substrate by ribosome-associated quality control. Our results provide insight into the causes and consequences of ribosome pause by dissecting collided ribosomes. Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved. |
| PMC | PMC7746506 |
| PMID | 32375038 |
| 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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| SRR10493408 | PRJNA590355 | Homo sapiens | HEK293 | Ribo-Seq | Anisomycin |  |
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| SRR10493409 | PRJNA590355 | Homo sapiens | HEK293 | Ribo-Seq | Anisomycin | |
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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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