Guydosh et al. 2013 (PRJNA230577)
General Details
| Title | Ribosome profiling study of dom34 and hbs1 knockout strains using short (16-nt) and long (28-nt) monosome-protected footprints and disome-protected footprints |
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| Organism | |
| Number of Samples | 29 |
| Release Date | 2013/12/04 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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| Visit Trips-Viz |
Repository Details
| SRA | SRP033499 |
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| ENA | SRP033499 |
| GEO | GSE52968 |
| BioProject | PRJNA230577 |
Publication
| Title | |
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| Authors | Guydosh NR,Green R |
| Journal | Cell |
| Publication Date | 2014 Feb 27 |
| Abstract | Ribosomes that stall before completing peptide synthesis must be recycled and returned to the cytoplasmic pool. The protein Dom34 and cofactors Hbs1 and Rli1 can dissociate stalled ribosomes in vitro, but the identity of targets in the cell is unknown. Here, we extend ribosome profiling methodology to reveal a high-resolution molecular characterization of Dom34 function in vivo. Dom34 removes stalled ribosomes from truncated mRNAs, but, in contrast, does not generally dissociate ribosomes on coding sequences known to trigger stalling, such as polyproline. We also show that Dom34 targets arrested ribosomes near the ends of 3' UTRs. These ribosomes appear to gain access to the 3' UTR via a mechanism that does not require decoding of the mRNA. These results suggest that ribosomes frequently enter downstream noncoding regions and that Dom34 carries out the important task of rescuing them. Copyright © 2014 Elsevier Inc. All rights reserved. |
| PMC | PMC4022138 |
| PMID | 24581494 |
| 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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| SRR1042853 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide |  |
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| SRR1042854 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042855 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | |
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| SRR1042856 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | |
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| SRR1042857 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042858 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | |
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| SRR1042859 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | |
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| SRR1042860 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042861 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | |
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| SRR1042862 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | |
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| SRR1042863 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042864 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042865 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042866 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042867 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042868 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042869 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042870 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042871 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042872 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042873 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042874 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042875 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042878 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042879 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | Cycloheximide | |
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| SRR1042880 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | |
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| SRR1042881 | PRJNA230577 | Saccharomyces cerevisiae | Ribo-Seq | |
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| SRR1042876 | PRJNA230577 | Saccharomyces cerevisiae | RNA-Seq | Cycloheximide | |
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| SRR1042877 | PRJNA230577 | Saccharomyces cerevisiae | 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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