Effects of sequence motifs in the yeast 3' untranslated region determined from massively parallel assays of random sequences.
Effects of sequence motifs in the yeast 3' untranslated region determined from massively parallel assays of random sequences.
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从随机序列的大规模平行分析确定酵母3‘非翻译区的序列基序的影响。
DOI：
10.1186/s13059-021-02509-6
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发表时间：
2021-10-18
期刊：
影响因子：
12.3
通讯作者：
Fields S
中科院分区：
文献类型：
--
作者：
Savinov A;Brandsen BM;Angell BE;Cuperus JT;Fields S
3′端非翻译区（UTR）通过影响mRNA的稳定性和翻译等活动，在决定基因表达水平方面起着关键作用。该区域内的功能元件已在很大程度上通过分析天然基因来鉴定，天然基因包含多个共同进化的序列特征。为了探索天然序列背景之外的3′ UTR序列元件的影响，我们分析了数十万个随机插入酵母酿酒酵母中报告基因3′ UTR的50-mer。我们从生长选择中转化体的适应性确定相对蛋白质表达水平。我们发现，共有3′ UTR效率元件显着提高表达，独立于序列上下文;另一方面，共有定位元件对表达只有很小的影响。作为Puf蛋白结合位点的一些序列基序显著增加文库中的表达，尽管这些蛋白通常与天然mRNA的转录后下调相关。我们的测量还允许系统地检查跨不同序列背景的效率元件基序内的点突变的影响。这些突变扫描揭示了效率元件中单个碱基的相对体内重要性，这可能反映了它们在结合参与切割和聚腺苷酸化的Hrp 1蛋白中的作用。一些3′ UTR序列特征的调节作用，如效率元件，是一致的，无论序列背景如何。相比之下，其他3′ UTR特征的结果似乎强烈依赖于它们在天然基因中的进化背景。在线版本包含补充材料，可通过10.1186/s13059-021-02509-6获得。
The 3′ untranslated region (UTR) plays critical roles in determining the level of gene expression through effects on activities such as mRNA stability and translation. Functional elements within this region have largely been identified through analyses of native genes, which contain multiple co-evolved sequence features. To explore the effects of 3′ UTR sequence elements outside of native sequence contexts, we analyze hundreds of thousands of random 50-mers inserted into the 3′ UTR of a reporter gene in the yeast Saccharomyces cerevisiae. We determine relative protein expression levels from the fitness of transformants in a growth selection. We find that the consensus 3′ UTR efficiency element significantly boosts expression, independent of sequence context; on the other hand, the consensus positioning element has only a small effect on expression. Some sequence motifs that are binding sites for Puf proteins substantially increase expression in the library, despite these proteins generally being associated with post-transcriptional downregulation of native mRNAs. Our measurements also allow a systematic examination of the effects of point mutations within efficiency element motifs across diverse sequence backgrounds. These mutational scans reveal the relative in vivo importance of individual bases in the efficiency element, which likely reflects their roles in binding the Hrp1 protein involved in cleavage and polyadenylation. The regulatory effects of some 3′ UTR sequence features, like the efficiency element, are consistent regardless of sequence context. In contrast, the consequences of other 3′ UTR features appear to be strongly dependent on their evolved context within native genes. The online version contains supplementary material available at 10.1186/s13059-021-02509-6.
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DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
14.8
作者：
Gietz, R. Daniel;Schiestl, Robert H.
通讯作者：
Schiestl, Robert H.
影响因子：
64.5
作者：
Geisberg JV;Moqtaderi Z;Fan X;Ozsolak F;Struhl K
通讯作者：
Struhl K
影响因子：
11.4
作者：
ABE, A;HIRAOKA, Y;FUKASAWA, T
通讯作者：
FUKASAWA, T
影响因子：
48
作者：
Gibson, Daniel G.;Young, Lei;Smith, Hamilton O.
通讯作者：
Smith, Hamilton O.