Ganesan et al. 2022 (PRJNA776169)
General Details
| Title | Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance |
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| Organism | |
| Number of Samples | 71 |
| Release Date | 2021/10/28 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP343728 |
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| ENA | SRP343728 |
| GEO | GSE186795 |
| BioProject | PRJNA776169 |
Publication
| Title | |
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| Authors | Ganesan R, Mangkalaphiban K, Baker RE, He F, Jacobson A |
| Journal | RNA (New York, N.Y.) |
| Publication Date | 2022 Dec |
| Abstract | Upf1, Upf2, and Upf3, the central regulators of nonsense-mediated mRNA decay (NMD), appear to exercise their NMD functions while bound to elongating ribosomes, and evidence for this conclusion is particularly compelling for Upf1. Hence, we used selective profiling of yeast Upf1:ribosome association to define that step in greater detail, understand whether the nature of the mRNA being translated influences Upf1:80S interaction, and elucidate the functions of ribosome-associated Upf1. Our approach has allowed us to clarify the timing and specificity of Upf1 association with translating ribosomes, obtain evidence for a Upf1 mRNA surveillance function that precedes the activation of NMD, identify a unique ribosome state that generates 37-43 nt ribosome footprints whose accumulation is dependent on Upf1's ATPase activity, and demonstrate that a mutated form of Upf1 can interfere with normal translation termination and ribosome release. In addition, our results strongly support the existence of at least two distinct functional Upf1 complexes in the NMD pathway. © 2022 Ganesan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society. |
| PMC | PMC9670811 |
| PMID | 36192133 |
| 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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| SRR16633390 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide |  |
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| SRR16633391 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633392 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633393 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633394 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633395 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633396 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633397 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633398 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633399 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633400 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633401 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633402 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633403 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633404 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633405 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633406 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633407 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633408 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633409 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633410 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633411 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633412 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633413 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633414 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633415 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633416 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633417 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633418 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633419 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633420 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633421 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633422 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633423 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633424 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633425 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633426 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633427 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633428 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633429 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633430 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633431 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633432 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633433 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633434 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633435 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633436 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633437 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633438 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633439 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633440 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633441 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633442 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | Ribo-Seq | Cycloheximide | |
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| SRR16633443 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633444 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633445 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633446 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633447 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633448 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633449 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633450 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633451 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633452 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633453 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633454 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633455 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633456 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633457 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633458 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633459 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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| SRR16633460 | PRJNA776169 | Saccharomyces cerevisiae | 0.0 | RNA-Seq | Cycloheximide | |
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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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