|
| Status |
Public on Jan 25, 2017 |
| Title |
eIF1 modulates the recognition of sub-optimal translation start sites and steers gene expression control mediated by uORFs |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Alternative translation initiation mechanisms such as leaky scanning and reinitiation potentiate the polycistronic nature of transcripts. By allowing for reprogrammed translation, these mechanisms can mediate biological responses to stress stimuli. We combined proteomics with ribosome profiling and mRNA sequencing to identify the biological targets of translation control triggered by eukaryotic translation initiation factor 1 (eIF1), a protein implicated in the stringency of start codon selection. We quantified expression changes of over 4,000 proteins and 10,000 actively translated transcripts, leading to the identification of 245 transcripts undergoing translational control mediated by upstream open reading frames (uORFs) upon eIF1 deprivation. The stringency of start codon selection and preference for optimal nucleotide context were largely diminished leading to translational regulation of uORFs with sub-optimal start sites. Affected genes were implicated in energy production and sensing of metabolic stress. Interestingly, knockdown of eIF1 elicited a synergic response from eIF5 and eIF1B.
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| |
|
| Overall design |
Ribosome profiling and mRNA sequening of human HCT116 cells upon eIF1 knockdown and in control conditions.
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| |
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| Contributor(s) |
Fijałkowska D, Verbruggen S, Ndah E, Jonckheere V, Tanco S, Menschaert G, Van Damme P |
| Citation(s) |
28541577 |
| Submission date |
Sep 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Petra Van Damme |
| E-mail(s) |
Petra.VanDamme@UGent.be
|
| Phone |
+32 9 264 9279
|
| Organization name |
University of Gent
|
| Department |
Department of Biochemistry
|
| Lab |
Kris Gevaert Lab
|
| Street address |
Albert Baertsoenkaai 3
|
| City |
Gent |
| State/province |
East Flanders |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (6)
|
| GSM2327825 |
Ribosome profiling of HCT116 cells upon eIF1 knockdown treated with lactimidomycin |
| GSM2327826 |
Ribosome profiling of HCT116 cells upon eIF1 knockdown treated with cycloheximide |
| GSM2327827 |
Ribosome profiling of control HCT116 cells treated with lactimidomycin |
| GSM2327828 |
Ribosome profiling of control HCT116 cells treated with cycloheximide |
| GSM2327829 |
mRNA sequencing of HCT116 cells upon eIF1 knockdown |
| GSM2327830 |
mRNA sequencing of control HCT116 cells |
|
| Relations |
| BioProject |
PRJNA344393 |
| SRA |
SRP090415 |
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