Zinshteyn et al. 2015 (PRJNA193543)

General Details

Title Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling
Organism
Number of Samples 8
Release Date 2013/03/20 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP019833
ENA SRP019833
GEO GSE45366
BioProject PRJNA193543

Publication

Title
Authors Zinshteyn B, Gilbert WV
Journal PLoS genetics
Publication Date 2013
Abstract Transfer RNA (tRNA) modifications enhance the efficiency, specificity and fidelity of translation in all organisms. The anticodon modification mcm(5)s(2)U(34) is required for normal growth and stress resistance in yeast; mutants lacking this modification have numerous phenotypes. Mutations in the homologous human genes are linked to neurological disease. The yeast phenotypes can be ameliorated by overexpression of specific tRNAs, suggesting that the modifications are necessary for efficient translation of specific codons. We determined the in vivo ribosome distributions at single codon resolution in yeast strains lacking mcm(5)s(2)U. We found accumulations at AAA, CAA, and GAA codons, suggesting that translation is slow when these codons are in the ribosomal A site, but these changes appeared too small to affect protein output. Instead, we observed activation of the GCN4-mediated stress response by a non-canonical pathway. Thus, loss of mcm(5)s(2)U causes global effects on gene expression due to perturbation of cellular signaling.
PMC PMC3731203
PMID 23935536
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR788070 PRJNA193543 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR788071 PRJNA193543 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR788072 PRJNA193543 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR788073 PRJNA193543 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR788074 PRJNA193543 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR788075 PRJNA193543 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR788076 PRJNA193543 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR788077 PRJNA193543 Saccharomyces cerevisiae 0.0 Ribo-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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