Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides [Dataset 5]

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 treatment globally alters gene expression with substantial effects on translation of histone genes, selenoprotein genes, and S-adenosylmethionine decarboxylase (AMD1). 2 ribosome profiling and 4 RNA-seq samples are included from Calu-6 cells

终止密码子通读（Stop codon readthrough, SCR）指核糖体在终止密码子处发生错码通读的现象。当关键基因中存在提前终止密码子（premature termination codon, PTC）时，这类通读事件具备治疗应用价值。为在全基因组水平开展体内SCR研究，我们采用氨基糖苷类试剂处理哺乳动物细胞，并开展了核糖体谱分析（ribosome profiling）。研究结果显示，氨基糖苷类除可刺激提前终止密码子的通读外，还能在全基因组范围内促进正常终止密码子（normal termination codon, NTC）的通读。终止密码子的类型、紧随其后的核苷酸以及周边mRNA序列环境，均会影响SCR的发生概率。相较于正常终止密码子，位于3'非翻译区（3' untranslated region, 3'UTR）的下游终止密码子更难被核糖体识别，这表明靶向关键终止密码子实现通读，或可避免广泛干扰翻译终止过程。最后，我们发现G418处理会全局性改变基因表达谱，对组蛋白基因、硒蛋白基因以及S-腺苷甲硫氨酸脱羧酶（AMD1）的翻译产生显著影响。本数据集包含来自Calu-6细胞的2份核糖体谱分析样本与4份RNA测序（RNA-seq）样本。