Mohammad et al. 2016 (PRJNA295296)
General Details
Title | Clarifying the translational pausing landscape in bacteria by ribosome profiling |
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Organism | |
Number of Samples | 3 |
Release Date | 2015/09/10 00:00 |
Sequencing Types | |
Protocol Details |
Study Links
GWIPS-viz | Trips-Viz |
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Repository Details
SRA | SRP063562 |
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ENA | SRP063562 |
GEO | GSE72899 |
BioProject | PRJNA295296 |
Publication
Title | |
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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) | ||
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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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