Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis
Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis
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DOI：
10.1073/pnas.1614788113
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发表时间：
2016-11-08
影响因子：
11.1
通讯作者：
Benfey, Philip N.
中科院分区：
文献类型：
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作者：
Hsu, Polly Yingshan;Calviello, Lorenzo;Benfey, Philip N.
核糖体足迹的深度测序（核糖体分析）绘制并量化mRNA翻译。由于核糖体每隔3 nt解码mRNA，因此核糖体足迹的周期性特性可用于鉴定新的翻译ORF。然而，由于现有方法的分辨率有限，3-nt周期性主要在全局分析中观察到，而不是在单个转录本中观察到。在这里，我们报告了一个协议应用于拟南芥，映射超过90%的足迹的主要阅读框架，从而提供了超分辨率个人成绩单，以精确定义翻译区。所得数据不仅支持许多注释和预测的非经典翻译事件，而且还揭示了注释的非编码RNA和假基因中的小ORF。这些未注释的ORF中有相当一部分在进化上是保守的，有些产生稳定的蛋白质。因此，我们的研究为植物基因组学提供了宝贵的资源，并为其他生物的核糖体分析提供了有效的优化策略。
Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied to Arabidopsis that maps over 90% of the footprints to the main reading frame and thus offers super-resolution profiles for individual transcripts to precisely define translated regions. The resulting data not only support many annotated and predicted noncanonical translation events but also uncover small ORFs in annotated noncoding RNAs and pseudogenes. A substantial number of these unannotated ORFs are evolutionarily conserved, and some produce stable proteins. Thus, our study provides a valuable resource for plant genomics and an efficient optimization strategy for ribosome profiling in other organisms.