Bohlen et al. 2020 (PRJNA579539)
General Details
| Title | Selective 40S footprinting reveals that scanning ribosomes remain cap-tethered in human cells |
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| Organism | |
| Number of Samples | 56 |
| Release Date | 2019/10/25 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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| Visit Trips-Viz |
Repository Details
| SRA | SRP226993 |
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| ENA | SRP226993 |
| GEO | |
| BioProject | PRJNA579539 |
Publication
| Title | |
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| Authors | Bohlen J,Fenzl K,Kramer G,Bukau B,Teleman AA |
| Journal | Molecular cell |
| Publication Date | 2020 Aug 20 |
| Abstract | Translation regulation occurs largely during the initiation phase. Here, we develop selective 40S footprinting to visualize initiating 40S ribosomes on endogenous mRNAs in vivo. This reveals the positions on mRNAs where initiation factors join the ribosome to act and where they leave. We discover that in most human cells, most scanning ribosomes remain attached to the 5' cap. Consequently, only one ribosome scans a 5' UTR at a time, and 5' UTR length affects translation efficiency. We discover that eukaryotic initiation factor 3B (eIF3B,) eIF4G1, and eIF4E remain bound to 80S ribosomes as they begin translating, with a decay half-length of ∼12 codons. Hence, ribosomes retain these initiation factors while translating short upstream open reading frames (uORFs), providing an explanation for how ribosomes can reinitiate translation after uORFs in humans. This method will be of use for studying translation initiation mechanisms in vivo. Copyright © 2020 Elsevier Inc. All rights reserved. |
| PMC | |
| PMID | 32589966 |
| 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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| SRR11549049 | PRJNA579539 | Mus musculus | 3T3 | SSU |  |
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| SRR11549050 | PRJNA579539 | Mus musculus | 3T3 | SSU | Harringtonine | |
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| SRR11549051 | PRJNA579539 | Mus musculus | 3T3 | SSU | Harringtonine | |
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| SRR11549052 | PRJNA579539 | Mus musculus | 3T3 | SSU | |
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| SRR11549053 | PRJNA579539 | Mus musculus | 3T3 | LSU | |
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| SRR11549054 | PRJNA579539 | Mus musculus | 3T3 | LSU | Harringtonine | |
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| SRR11549055 | PRJNA579539 | Mus musculus | 3T3 | LSU | Harringtonine | |
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| SRR11549056 | PRJNA579539 | Mus musculus | 3T3 | LSU | |
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| SRR11549065 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR11549066 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR11549067 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR11549057 | PRJNA579539 | Mus musculus | 3T3 | RNA-Seq | |
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| SRR11549058 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR11549059 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR11549060 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR11549061 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR11549062 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR11549063 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR11549064 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346262 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346263 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346264 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346265 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346266 | PRJNA579539 | Homo sapiens | RNA-Seq | |
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| SRR10346267 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346268 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346269 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346270 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346271 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346272 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346273 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346274 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346275 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346276 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346277 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346278 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346279 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346280 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346283 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346284 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346285 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346286 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346287 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346288 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346289 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346290 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346291 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346292 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346295 | PRJNA579539 | Homo sapiens | SSU | |
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| SRR10346296 | PRJNA579539 | Homo sapiens | SSU | Harringtonine | |
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| SRR10346297 | PRJNA579539 | Homo sapiens | SSU | Harringtonine | |
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| SRR10346298 | PRJNA579539 | Homo sapiens | SSU | Harringtonine | |
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| SRR10346299 | PRJNA579539 | Homo sapiens | LSU | |
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| SRR10346300 | PRJNA579539 | Homo sapiens | LSU | Harringtonine | |
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| SRR10346301 | PRJNA579539 | Homo sapiens | LSU | Harringtonine | |
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| SRR10346302 | PRJNA579539 | Homo sapiens | LSU | Harringtonine | |
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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) |
ⓘ For more Information on the columns shown here see: About