Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast

Despite being predicted to lack coding potential, cytoplasmic long non-coding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNAs translation remains poorly studied. In yeast, cytoplasmic Xrn1-sensitive lncRNAs (XUTs) are targeted by the Nonsense-Mediated mRNA Decay (NMD), suggesting a translation-dependent degradation process. Here, we report that XUTs are pervasively translated, which impacts their decay. We show that XUTs globally accumulate upon translation elongation inhibition, but not when initial ribosome loading is impaired. Ribo-Seq confirmed ribosomes binding to XUTs and identified ribosome-associated 5’-proximal small ORFs. Mechanistically, the NMD-sensitivity of XUTs mainly depends on the 3’-untranslated region length. Finally, we show that the peptide resulting from the translation of an NMD-sensitive XUT reporter exists in NMD-competent cells. Our work highlights the role of translation in the post-transcriptional metabolism of XUTs. We propose that XUT-derived peptides could be exposed to the natural selection, while NMD restricts XUTs levels. Refer to individual Series尽管此前学界预测细胞质长链非编码RNA（lncRNA）不具备编码潜能，但这类RNA却可与核糖体结合。然而，有关长链非编码RNA翻译的整体图景及其生物学相关性，目前仍缺乏深入研究。在酵母中，受细胞质Xrn1核酸酶敏感的长链非编码RNA（XUTs）会被无义介导的mRNA降解（Nonsense-Mediated mRNA Decay, NMD）通路靶向，这提示其降解过程依赖翻译机制。本研究证实XUTs可被广泛翻译，并会对其自身降解产生影响。我们发现，当翻译延伸过程受到抑制时，XUTs的全局表达量会显著积累；而当核糖体初始装载过程受损时，则无此现象。核糖体测序（Ribo-Seq）结果证实了核糖体与XUTs的结合，并鉴定出了核糖体关联的5’端近端小型开放阅读框（ORF）。从机制层面来看，XUTs对NMD的敏感性主要取决于其3’非翻译区（3’UTR）的长度。最后，我们证明了携带NMD敏感型XUT报告基因的翻译产物肽段，可在具备NMD通路活性的细胞中稳定存在。本研究揭示了翻译过程在XUTs转录后代谢中的关键作用。我们提出，XUTs翻译产生的肽段可能会受到自然选择的作用，而NMD通路则会限制XUTs的表达水平。具体详情请参见各数据集系列。