Gu et al. 2021 (PRJNA734658)

General Details

Title Bi-directional ribosome scanning controls the stringency of start codon selection
Organism
Number of Samples 22
Release Date 2021/06/02 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP322410
ENA SRP322410
GEO
BioProject PRJNA734658

Publication

Title
Authors Gu Y,Mao Y,Jia L,Dong L,Qian SB
Journal Nature communications
Publication Date 2021 Nov 15
Abstract The fidelity of start codon recognition by ribosomes is paramount during protein synthesis. The current knowledge of eukaryotic translation initiation implies unidirectional 5'→3' migration of the pre-initiation complex (PIC) along the 5' UTR. In probing translation initiation from ultra-short 5' UTR, we report that an AUG triplet near the 5' end can be selected via PIC backsliding. Bi-directional ribosome scanning is supported by competitive selection of closely spaced AUG codons and recognition of two initiation sites flanking an internal ribosome entry site. Transcriptome-wide PIC profiling reveals footprints with an oscillation pattern near the 5' end and start codons. Depleting the RNA helicase eIF4A leads to reduced PIC oscillations and impaired selection of 5' end start codons. Enhancing the ATPase activity of eIF4A promotes nonlinear PIC scanning and stimulates upstream translation initiation. The helicase-mediated PIC conformational switch may provide an operational mechanism that unifies ribosome recruitment, scanning, and start codon selection. © 2021. The Author(s).
PMC PMC8593136
PMID 34782646
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR14714407 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714408 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714409 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714410 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714411 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714412 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714413 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714414 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714415 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714416 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714417 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714418 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714419 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714420 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR14714421 PRJNA734658 Homo sapiens HEK293 Ribo-Seq
SRR14714422 PRJNA734658 Homo sapiens HEK293 Ribo-Seq
SRR14714423 PRJNA734658 Homo sapiens HEK293 Ribo-Seq
SRR14714424 PRJNA734658 Homo sapiens HEK293 Ribo-Seq
SRR14714425 PRJNA734658 Homo sapiens HEK293 Ribo-Seq
SRR14714426 PRJNA734658 Homo sapiens HEK293 Ribo-Seq
SRR16077415 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
SRR16077416 PRJNA734658 Mus musculus Mouse embryonic fibroblasts Ribo-Seq
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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