Developmental regulation of Canonical and small ORF translation from mRNAs
Developmental regulation of Canonical and small ORF translation from mRNAs
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mRNA 的规范和小 ORF 翻译的发育调控
DOI：
10.1101/727339
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Patraquim P
中科院分区：
文献类型：
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作者：
Patraquim P
背景核糖体分析揭示了注释的蛋白质编码基因外的数千个序列的翻译，包括小于100个密码子的小开放阅读框架，以及许多基因的翻译调控。在这里，我们提出了一个改进版本的聚核糖测序和应用它tosophila melanogasterembryos在体内翻译的小ORF的目录扩展，并揭示跨embryogenesis.ResultsWe获得高度相关的样品在五个胚胎阶段，近5亿推定的核糖体足迹映射到mRNA的小和典型的ORF的翻译调控，并将其与现有的Ribo-Seq和蛋白质组数据进行比较。我们的分析第一次揭示了果蝇的足迹以阶段性模式映射到密码子，这是生产性翻译的标志。我们提出了一个简单的二项式概率度量来确定翻译概率。我们的研究结果还揭示了可重复的核糖体结合显然不会导致生产性翻译。这种非生产性的核糖体结合似乎是特别普遍的上游短ORF位于5′ mRNA的领导人，其中典型的ORF在激活合子translatome在maternal-to-zygotictransition.ConclusionsWe建议，这种非生产性的核糖体结合可能是由于顺式调节核糖体结合和有缺陷的核糖体扫描的ORF生产性翻译以外的时期。我们的研究结果是兼容的上游短ORF的主要功能是缓冲典型的典型ORF的翻译，并表明，在一般情况下，小的ORF在mRNA显示标记兼容的进化过渡状态向完整的编码功能。
BackgroundRibosomal profiling has revealed the translation of thousands of sequences outside annotated protein-coding genes, including small open reading frames of less than 100 codons, and the translational regulation of many genes. Here we present an improved version of Poly-Ribo-Seq and apply it toDrosophila melanogasterembryos to extend the catalog of in vivo translated small ORFs, and to reveal the translational regulation of both small and canonical ORFs from mRNAs across embryogenesis.ResultsWe obtain highly correlated samples across five embryonic stages, with nearly 500 million putative ribosomal footprints mapped to mRNAs, and compare them to existing Ribo-Seq and proteomic data. Our analysis reveals, for the first time inDrosophila, footprints mapping to codons in a phased pattern, the hallmark of productive translation. We propose a simple binomial probability metric to ascertain translation probability. Our results also reveal reproducible ribosomal binding apparently not resulting in productive translation. This non-productive ribosomal binding seems to be especially prevalent amongst upstream short ORFs located in the 5′ mRNA leaders, and amongst canonical ORFs during the activation of the zygotic translatome at the maternal-to zygotic transition.ConclusionsWe suggest that this non-productive ribosomal binding might be due to cis-regulatory ribosomal binding and to defective ribosomal scanning of ORFs outside periods of productive translation. Our results are compatible with the main function of upstream short ORFs being to buffer the translation of canonical canonical ORFs; and show that, in general, small ORFs in mRNAs display markers compatible with an evolutionary transitory state towards full coding function.