Wangen et al. 2020 (PRJNA576653)

General Details

Title Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides [Dataset 5]
Organism
Number of Samples 2
Release Date 2019/10/09 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP224956
ENA SRP224956
GEO GSE138642
BioProject PRJNA576653

Publication

Title
Authors Wangen JR,Green R
Journal eLife
Publication Date 2020 Jan 23
Abstract Stop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough events can be therapeutically desirable when a premature termination codon (PTC) is found in a critical gene. To study SCR in vivo in a genome-wide manner, we treated mammalian cells with aminoglycosides and performed ribosome profiling. We find that in addition to stimulating readthrough of PTCs, aminoglycosides stimulate readthrough of normal termination codons (NTCs) genome-wide. Stop codon identity, the nucleotide following the stop codon, and the surrounding mRNA sequence context all influence the likelihood of SCR. In comparison to NTCs, downstream stop codons in 3'UTRs are recognized less efficiently by ribosomes, suggesting that targeting of critical stop codons for readthrough may be achievable without general disruption of translation termination. Finally, we find that G418-induced miscoding alters gene expression with substantial effects on translation of histone genes, selenoprotein genes, and S- adenosylmethionine decarboxylase (AMD1). © 2020, Wangen and Green.
PMC PMC7089771
PMID 31971508
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR10251308 PRJNA576653 Homo sapiens Calu-6 cells Ribo-Seq untreated
SRR10251309 PRJNA576653 Homo sapiens Calu-6 cells 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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