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Series GSE139391 Query DataSets for GSE139391
Status Public on Jun 25, 2020
Title Selective 40S footprinting reveals that scanning ribosomes remain cap-tethered in human cells
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Other
Summary Translation regulation occurs largely during initiation. Currently, translation initiation can be studied in vitro, but these systems lack features present in vivo and on endogenous mRNAs. Here we develop selective 40S footprinting for visualizing initiating 40S ribosomes on endogenous mRNAs in vivo. It pinpoints where on an mRNA initiation factors join the ribosome to act, and where they leave. We discover that in human cells most scanning ribosomes remain attached to the 5’ cap. Consequently, only one ribosome scans a 5’UTR at a time, and 5’UTR length affects translation efficiency. We discover that eIF3B, eIF4G1 and eIF4E remain on translating 80S ribosomes with a decay half-length of ~12 codons. Hence ribosomes retain these initiation factors while translating short upstream Open Reading Frames (uORFs), providing an explanation for how ribosomes can re-initiate translation after uORFs in humans. This method will be of use for studying translation initiation mechanisms in vivo.
 
Overall design Selective and total 40S and 80S footprinting was carried out on HeLa and NIH3T3 cells. Selective datasets were produced for factors eIF3B, eIF4E, eIF2S1 and eIF4G1.
 
Contributor(s) Bohlen J, Teleman A
Citation(s) 32589966, 36869665
Submission date Oct 25, 2019
Last update date May 12, 2023
Contact name Jonathan Bohlen
Organization name DKFZ
Department B140
Lab AG Teleman
Street address Im Neuenheimer Feld 581
City Heidelberg
ZIP/Postal code 69123
Country Germany
 
Platforms (2)
GPL21626 NextSeq 550 (Mus musculus)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (60)
GSM4140413 Total 40S Ribosome FPs Hela cells [1_40S_Total]
GSM4140414 eiF3B Selective 40S Ribosome FPs Hela Cells [1_40S_eiF3B]
GSM4140415 Total 80S Ribosome FPs Hela cells [1_80S_Total]
Relations
BioProject PRJNA579539
SRA SRP226993

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE139391_Master_Data_Table.xlsx 19.8 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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