Sen et al. 2015 (PRJNA276827)

General Details

Title Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A
Organism
Number of Samples 16
Release Date 2015/03/02 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP055707
ENA SRP055707
GEO
BioProject PRJNA276827

Publication

Title
Authors Sen ND,Zhou F,Ingolia NT,Hinnebusch AG
Journal Genome research
Publication Date 2015 Aug
Abstract DEAD-box RNA helicases eIF4A and Ded1 are believed to promote translation initiation by resolving mRNA secondary structures that impede ribosome attachment at the mRNA 5' end or subsequent scanning of the 5' UTR, but whether they perform unique or overlapping functions in vivo is poorly understood. We compared the effects of mutations in Ded1 or eIF4A on global translational efficiencies (TEs) in budding yeast Saccharomyces cerevisiae by ribosome footprint profiling. Despite similar reductions in bulk translation, inactivation of a cold-sensitive Ded1 mutant substantially reduced the TEs of >600 mRNAs, whereas inactivation of a temperature-sensitive eIF4A variant encoded by tif1-A79V (in a strain lacking the ortholog TIF2) yielded <40 similarly impaired mRNAs. The broader requirement for Ded1 did not reflect more pervasive secondary structures at low temperature, as inactivation of temperature-sensitive and cold-sensitive ded1 mutants gave highly correlated results. Interestingly, Ded1-dependent mRNAs exhibit greater than average 5' UTR length and propensity for secondary structure, implicating Ded1 in scanning through structured 5' UTRs. Reporter assays confirmed that cap-distal stem-loop insertions increase dependence on Ded1 but not eIF4A for efficient translation. While only a small fraction of mRNAs shows a heightened requirement for eIF4A, dependence on eIF4A is correlated with requirements for Ded1 and 5' UTR features characteristic of Ded1-dependent mRNAs. Our findings suggest that Ded1 is critically required to promote scanning through secondary structures within 5' UTRs, and while eIF4A cooperates with Ded1 in this function, it also promotes a step of initiation common to virtually all yeast mRNAs. © 2015 Sen et al.; Published by Cold Spring Harbor Laboratory Press.
PMC PMC4510003
PMID 26122911
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR1822445 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822446 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822447 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822448 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822453 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822454 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822455 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822456 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822461 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822462 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822463 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822464 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822469 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822470 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822471 PRJNA276827 Saccharomyces cerevisiae Ribo-Seq Cycloheximide
SRR1822472 PRJNA276827 Saccharomyces cerevisiae 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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