Bohlen et al. 2020 (PRJNA579539)

General Details

Title Selective 40S footprinting reveals that scanning ribosomes remain cap-tethered in human cells
Organism
Number of Samples 56
Release Date 2019/10/25 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP226993
ENA SRP226993
GEO GSE139391
BioProject PRJNA579539

Publication

Title
Authors Bohlen J, Fenzl K, Kramer G, Bukau B, Teleman AA
Journal Molecular cell
Publication Date 2020 Aug 20
Abstract Translation regulation occurs largely during the initiation phase. Here, we develop selective 40S footprinting to visualize initiating 40S ribosomes on endogenous mRNAs in vivo. This reveals the positions on mRNAs where initiation factors join the ribosome to act and where they leave. We discover that in most 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 eukaryotic initiation factor 3B (eIF3B,) eIF4G1, and eIF4E remain bound to 80S ribosomes as they begin translating, 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 reinitiate translation after uORFs in humans. This method will be of use for studying translation initiation mechanisms in vivo. Copyright © 2020 Elsevier Inc. All rights reserved.
PMC
PMID 32589966
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR11549049 PRJNA579539 Mus musculus 3T3 SSU 0.0
SRR11549050 PRJNA579539 Mus musculus 3T3 SSU Harringtonine
SRR11549051 PRJNA579539 Mus musculus 3T3 SSU Harringtonine
SRR11549052 PRJNA579539 Mus musculus 3T3 SSU 0.0
SRR11549053 PRJNA579539 Mus musculus 3T3 LSU 0.0
SRR11549054 PRJNA579539 Mus musculus 3T3 LSU Harringtonine
SRR11549055 PRJNA579539 Mus musculus 3T3 LSU Harringtonine
SRR11549056 PRJNA579539 Mus musculus 3T3 LSU 0.0
SRR11549065 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR11549066 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR11549067 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR11549057 PRJNA579539 Mus musculus 3T3 RNA-Seq 0.0
SRR11549058 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR11549059 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR11549060 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR11549061 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR11549062 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR11549063 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR11549064 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346262 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346263 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346264 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346265 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346266 PRJNA579539 Homo sapiens HeLa RNA-Seq 0.0
SRR10346267 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346268 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346269 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346270 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346271 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346272 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346273 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346274 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346275 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346276 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346277 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346278 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346279 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346280 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346283 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346284 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346285 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346286 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346287 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346288 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346289 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346290 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346291 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346292 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346295 PRJNA579539 Homo sapiens HeLa SSU 0.0
SRR10346296 PRJNA579539 Homo sapiens HeLa SSU Harringtonine
SRR10346297 PRJNA579539 Homo sapiens HeLa SSU Harringtonine
SRR10346298 PRJNA579539 Homo sapiens HeLa SSU Harringtonine
SRR10346299 PRJNA579539 Homo sapiens HeLa LSU 0.0
SRR10346300 PRJNA579539 Homo sapiens HeLa LSU Harringtonine
SRR10346301 PRJNA579539 Homo sapiens HeLa LSU Harringtonine
SRR10346302 PRJNA579539 Homo sapiens HeLa LSU Harringtonine
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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