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
Organism
Number of Samples 29
Release Date 2013/12/04 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP033499
ENA SRP033499
GEO GSE52968
BioProject PRJNA230577

Publication

Title
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)
SRR1042853 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042854 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042855 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Frozen
SRR1042856 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Frozen
SRR1042857 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042858 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq 0.0
SRR1042859 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq 0.0
SRR1042860 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042861 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq 0.0
SRR1042862 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq 0.0
SRR1042863 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042864 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042865 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042866 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042867 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042868 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042869 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042870 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042871 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042872 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042873 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042874 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042875 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042878 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042879 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042880 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042881 PRJNA230577 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR1042876 PRJNA230577 Saccharomyces cerevisiae 0.0 RNA-Seq Cycloheximide
SRR1042877 PRJNA230577 Saccharomyces cerevisiae 0.0 RNA-Seq Cycloheximide
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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