Wangen et al. 2020 (PRJNA576649)

General Details

Title Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides [Dataset 1]
Organism
Number of Samples 18
Release Date 2019/10/09 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP224952
ENA SRP224952
GEO GSE138638
BioProject PRJNA576649

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)
SRR10251273 PRJNA576649 Homo sapiens HEK293 Ribo-Seq untreated
SRR10251274 PRJNA576649 Homo sapiens HEK293 Ribo-Seq untreated
SRR10251275 PRJNA576649 Homo sapiens HEK293 Ribo-Seq
SRR10251276 PRJNA576649 Homo sapiens HEK293 Ribo-Seq
SRR10251277 PRJNA576649 Homo sapiens HEK293 Ribo-Seq
SRR10251278 PRJNA576649 Homo sapiens HEK293 Ribo-Seq
SRR10251279 PRJNA576649 Homo sapiens HEK293 Ribo-Seq gentamicin
SRR10251280 PRJNA576649 Homo sapiens HEK293 Ribo-Seq gentamicin
SRR10251281 PRJNA576649 Homo sapiens HEK293 Ribo-Seq paromomycin
SRR10251282 PRJNA576649 Homo sapiens HEK293 Ribo-Seq paromomycin
SRR10251283 PRJNA576649 Homo sapiens HEK293 Ribo-Seq neomycin
SRR10251284 PRJNA576649 Homo sapiens HEK293 Ribo-Seq neomycin
SRR10251285 PRJNA576649 Homo sapiens HEK293 Ribo-Seq tobramycin
SRR10251286 PRJNA576649 Homo sapiens HEK293 Ribo-Seq tobramycin
SRR10251287 PRJNA576649 Homo sapiens HEK293 Ribo-Seq amikacin
SRR10251288 PRJNA576649 Homo sapiens HEK293 Ribo-Seq amikacin
SRR10251289 PRJNA576649 Homo sapiens HEK293 Ribo-Seq
SRR10251290 PRJNA576649 Homo sapiens HEK293 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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