A large fraction of genes contains upstream ORFs (uORFs) in the 5′ untranslated region (5’UTR). The translation of uORFs can inhibit the translation of the main coding sequence, for example by causing premature dissociation of the two ribosomal units or ribosome stalling. However, it is currently unknown if most uORFs are inhibitory or if this activity is restricted to specific cases. Here we interrogate ribosome profiling data from three different stress experiments in yeast to gain novel insights into this question. By comparing ribosome occupancies in different conditions and experiments we obtain strong evidence that, in comparison to primary coding sequences (CDS), which undergo translational arrest during stress, the translation of uORFs is mostly unaffected by changes in the environment. As a result, the relative abundance of uORF-encoded peptides increases during stress. In general, the changes in the translational efficiency of regions containing uORFs do not seem to affect downstream translation. The exception are uORFs found in a subset of genes that are significantly up-regulated at the level of translation during stress; these uORFs tend to be translated at lower levels in stress conditions than in optimal growth conditions, facilitating the translation of the CDS during stress. We find new examples of uORF-mediated regulation of translation, including the Gcn4 functional homologue fil1 and ubi4 genes in S. pombe. We find evidence that the relative amount of uORF-encoded peptides increases during stress. The increased translation of uORFs is however uncoupled from the general CDS translational repression observed during stress. In a subset of genes that encode proteins that need to be rapidly synthesized upon stress uORFs act as translational switches.

中文翻译：

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uORFs 在介导压力条件下翻译调节中的影响

大部分基因在 5' 非翻译区 (5'UTR) 中包含上游 ORF (uORF)。uORFs 的翻译可以抑制主要编码序列的翻译，例如通过导致两个核糖体单元的过早解离或核糖体停滞。然而，目前尚不清楚大多数 uORF 是否具有抑制性，或者这种活动是否仅限于特定情况。在这里，我们询问了来自酵母中三个不同压力实验的核糖体分析数据，以获得对这个问题的新见解。通过比较不同条件和实验中的核糖体占有率，我们获得了强有力的证据，即与在压力期间经历翻译停滞的初级编码序列 (CDS) 相比，uORFs 的翻译大多不受环境变化的影响。其结果，uORF 编码肽的相对丰度在压力期间增加。一般来说，含有 uORFs 的区域翻译效率的变化似乎不会影响下游翻译。例外是在一个基因子集中发现的 uORFs 在压力期间在翻译水平上显着上调；与最佳生长条件相比，这些 uORF 在压力条件下的翻译水平往往低于最佳生长条件，从而促进了 CDS 在压力下的翻译。我们发现了 uORF 介导的翻译调控的新例子，包括 S. pombe 中的 Gcn4 功能同源 fil1 和 ubi4 基因。我们发现证据表明 uORF 编码的肽的相对量在压力期间增加。然而，增加的 uORF 翻译与在压力期间观察到的一般 CDS 翻译抑制无关。