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Series GSE87328 Query DataSets for GSE87328
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
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.
Overall design Ribosome profiling and mRNA sequening of human HCT116 cells upon eIF1 knockdown and in control conditions.
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
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
BioProject PRJNA344393
SRA SRP090415

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Supplementary file Size Download File type/resource
GSE87328_RAW.tar 393.2 Mb (http)(custom) TAR (of BEDGRAPH)
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Raw data are available in SRA
Processed data provided as supplementary file

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