Mohammad et al. 2016 (PRJNA295296)

General Details

Title Clarifying the translational pausing landscape in bacteria by ribosome profiling
Organism
Number of Samples 3
Release Date 2015/09/10 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP063562
ENA SRP063562
GEO GSE72899
BioProject PRJNA295296

Publication

Title
Authors Mohammad F, Woolstenhulme CJ, Green R, Buskirk AR
Journal Cell reports
Publication Date 2016 Feb 2
Abstract The rate of protein synthesis varies according to the mRNA sequence in ways that affect gene expression. Global analysis of translational pausing is now possible with ribosome profiling. Here, we revisit an earlier report that Shine-Dalgarno sequences are the major determinant of translational pausing in bacteria. Using refinements in the profiling method as well as biochemical assays, we find that SD motifs have little (if any) effect on elongation rates. We argue that earlier evidence of pausing arose from two factors. First, in previous analyses, pauses at Gly codons were difficult to distinguish from pauses at SD motifs. Second, and more importantly, the initial study preferentially isolated long ribosome-protected mRNA fragments that are enriched in SD motifs. These findings clarify the landscape of translational pausing in bacteria as observed by ribosome profiling. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.
PMC PMC4835026
PMID 26776510
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR2340141 PRJNA295296 Escherichia coli 0.0 Ribo-Seq 0.0
SRR2340143 PRJNA295296 Escherichia coli 0.0 Ribo-Seq 0.0
SRR2340144 PRJNA295296 Escherichia coli 0.0 Ribo-Seq 0.0
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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