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| Status |
Public on Jan 25, 2023 |
| Title |
eIF4F complex dynamics are important for the activation of the integrated stress response |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In response to stress, eukaryotes activate the integrated stress response (ISR) via phosphorylation of eIF2α to promote the translation of pro-survival effector genes, such as GCN4 in yeast. Complementing the ISR is the Target of Rapamycin (TOR) pathway, which regulates eIF4E function. Here we probe translational control in the absence of eIF4E in Saccharomyces cerevisiae. Intriguingly, we find that loss of eIF4E leads to de-repression of GCN4 translation. In addition, we find that de-repression of GCN4 translation is neither accompanied by eIF2α phosphorylation nor reduction in initiator ternary complex. Our data suggest that when eIF4E levels are depleted, GCN4 translation is de-repressed via a unique mechanism that may involve faster scanning by the small ribosome subunit due to increased local concentration of eIF4A. Overall, our findings suggest that relative levels of eIF4F components are key to ribosome dynamics and may play important roles in translational control of gene expression.
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| Overall design |
Genome and Transcriptome Mapped ribosome profiling and RNA-seq reads. Genome mapping was done using STAR and analyzed using FeatureCounts and python scripts. Transcriptome mapping was done using Salmon and analyzed using DESeq2.
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| Contributor(s) |
Kim KQ, Nanjaraj Urs AN, Lashinde V, Greenlaw AC, Hudson BH, Zaher HS |
| Citation missing |
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| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM112641 |
Ribosome stalling and activation of stress responses |
WASHINGTON UNIVERSITY |
Hani Zaher |
| R01 GM141474 |
Reading frame maintenance by the ribosome during stalling |
WASHINGTON UNIVERSITY |
Hani Zaher |
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| Submission date |
Jan 23, 2023 |
| Last update date |
Apr 17, 2024 |
| Contact name |
Hani Zaher |
| E-mail(s) |
hzaher@wustl.edu
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| Organization name |
Washington University in St. Louis
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| Department |
Biology
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| Street address |
1 Brookings Drive
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| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63130 |
| Country |
USA |
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| Platforms (1) |
| GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
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| Samples (20)
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| GSM6956685 |
ribosome profiling, 37°C [rpf_ts_37_2] |
| GSM6956686 |
ribosome profiling, 25°C [rpf_wt_25_1] |
| GSM6956687 |
ribosome profiling, 25°C [rpf_wt_25_2] |
| GSM6956688 |
ribosome profiling, 37°C [rpf_wt_37_1] |
| GSM6956689 |
ribosome profiling, 37°C [rpf_wt_37_2] |
| GSM6956690 |
RNA-seq, 25°C [rna_ts_25_1] |
| GSM6956691 |
RNA-seq, 25°C [rna_ts_25_2] |
| GSM6956692 |
RNA-seq, 25°C [rna_ts_25_3] |
| GSM6956693 |
RNA-seq, 37°C [rna_ts_37_1] |
| GSM6956694 |
RNA-seq, 37°C [rna_ts_37_2] |
| GSM6956695 |
RNA-seq, 37°C [rna_ts_37_3] |
| GSM6956696 |
RNA-seq, 25°C [rna_wt_25_1] |
| GSM6956697 |
RNA-seq, 25°C [rna_wt_25_2] |
| GSM6956698 |
RNA-seq, 25°C [rna_wt_25_3] |
| GSM6956699 |
RNA-seq, 37°C [rna_wt_37_1] |
| GSM6956700 |
RNA-seq, 37°C [rna_wt_37_2] |
| GSM6956701 |
RNA-seq, 37°C [rna_wt_37_3] |
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| Relations |
| BioProject |
PRJNA926480 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE223465_DESeq2_Differential_Expression.xlsx |
4.2 Mb |
(ftp)(http) |
XLSX |
| GSE223465_Metagene_Analysis.xlsx |
2.0 Mb |
(ftp)(http) |
XLSX |
| GSE223465_Multivariate_Analysis.xlsx |
499.2 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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