Tesina et al. 2019 (PRJNA473989)

General Details

Title Regulation of Translation Elongation Revealed by Ribosome Profiling [Dataset_4]
Organism
Number of Samples 28
Release Date 2018/05/31 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP149446
ENA SRP149446
GEO GSE115161
BioProject PRJNA473989

Publication

Title
Authors Tesina P, Lessen LN, Buschauer R, Cheng J, Wu CC, Berninghausen O, Buskirk AR, Becker T, Beckmann R, Green R
Journal The EMBO journal
Publication Date 2020 Feb 3
Abstract Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro biochemistry, ribosome profiling, and cryo-EM to define molecular mechanisms that lead to these ribosome stalls. First, we use an in vitro reconstituted yeast translation system to demonstrate that inhibitory codon pairs slow elongation rates which are partially rescued by increased tRNA concentration or by an artificial tRNA not dependent on wobble base-pairing. Ribosome profiling data extend these observations by revealing that paused ribosomes with empty A sites are enriched on these sequences. Cryo-EM structures of stalled ribosomes provide a structural explanation for the observed effects by showing decoding-incompatible conformations of mRNA in the A sites of all studied stall- and collision-inducing sequences. Interestingly, in the case of poly(A) tracts, the inhibitory conformation of the mRNA in the A site involves a nucleotide stacking array. Together, these data demonstrate a novel mRNA-induced mechanisms of translational stalling in eukaryotic ribosomes. © 2019 The Authors.
PMC PMC6996574
PMID 31858614
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR7241910 PRJNA473989 Homo sapiens MDA Ribo-Seq Frozen
SRR7241911 PRJNA473989 Caenorhabditis elegans 0.0 Ribo-Seq Frozen
SRR7241912 PRJNA473989 Homo sapiens HeLa Ribo-Seq Frozen
SRR7241913 PRJNA473989 Homo sapiens HeLa Ribo-Seq Frozen
SRR7241914 PRJNA473989 Homo sapiens HeLa Ribo-Seq Frozen
SRR7241915 PRJNA473989 Homo sapiens HeLa Ribo-Seq Cycloheximide
SRR7241916 PRJNA473989 Homo sapiens HeLa Ribo-Seq Frozen
SRR13091900 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR7241918 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR7241919 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR7241920 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR7241922 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR7241923 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR7241924 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Frozen
SRR7241925 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Frozen
SRR7241926 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Frozen
SRR7241927 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Frozen
SRR7241928 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Frozen
SRR7241929 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Frozen
SRR7241930 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Frozen
SRR7241931 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Frozen
SRR7241932 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Frozen
SRR7241933 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Frozen
SRR8093855 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR8093856 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR8093857 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR8093858 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Cycloheximide
SRR8093859 PRJNA473989 Saccharomyces cerevisiae 0.0 Ribo-Seq Frozen
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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