Light is one of the most essential environmental clues for plant growth and morphogenesis. Exposure to blue monochromatic light from darkness is a turning point for plant biological activity, and as a result dramatic changes in gene expression occur. To understand the translational impacts of blue light, we have performed ribosome profiling analysis and called translated open reading frames (ORFs) de novo within not only mRNAs but also non-coding RNAs (ncRNAs). Translation efficiency of 3,823 protein-coding ORFs, such as nuclear chloroplast-related genes, was up-regulated by blue light exposure. Moreover, the translational activation of the microRNA biogenesis-related genes, DCL1 and HYL1, was induced by blue light. Considering the 3-nucleotide codon periodicity of ribosome footprints, a few hundred short ORFs lying on ncRNAs and upstream ORFs (uORFs) on mRNAs were found that had differential translation status between blue light and dark. uORFs are known to have a negative effect on the expression of the main ORFs (mORFs) on the same mRNAs. Our analysis suggests that the translation of uORFs is likely to be more stimulated than that of the corresponding mORFs, and uORF-mediated translational repression of the mORFs in five genes was alleviated by blue light exposure. With data-based annotation of the ORFs, our analysis provides insights into the translatome in response to environmental changes, such as those involving light.

中文翻译：

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拟南芥中光照后蛋白质编码和非蛋白质编码RNA的翻译景观。

光线是植物生长和形态发生的最重要的环境线索之一。从黑暗中暴露于蓝色单色光是植物生物活性的转折点，结果基因表达发生了巨大变化。为了了解蓝光的翻译影响，我们进行了核糖体谱分析，并不仅在mRNA中而且在非编码RNA（ncRNA）中也称为从头翻译的开放阅读框（ORF）。蓝光照射上调了3,823个编码蛋白质的ORF（如核叶绿体相关基因）的翻译效率。此外，蓝光诱导了与microRNA生物发生相关的基因DCL1和HYL1的翻译激活。考虑到核糖体足迹的3个核苷酸的密码子周期性，发现位于ncRNA上的数百个短ORF和位于mRNA上的上游ORF（uORF）在蓝光和暗光之间具有不同的翻译状态。已知uORF对相同mRNA上的主要ORF（mORF）的表达具有负面影响。我们的分析表明，uORFs的翻译可能比相应的mORFs受到更多的刺激，并且通过蓝光照射减轻了5个基因中uORF介导的mORFs的翻译抑制。借助基于数据的ORF注释，我们的分析可洞悉跨膜组以响应环境变化（例如涉及光的环境变化）。我们的分析表明，uORFs的翻译可能比相应的mORFs受到更多的刺激，并且通过蓝光照射减轻了5个基因中uORF介导的mORFs的翻译抑制。借助基于数据的ORF注释，我们的分析可洞悉跨膜组以响应环境变化（例如涉及光的环境变化）。我们的分析表明，uORFs的翻译可能比相应的mORFs受到更多的刺激，并且通过蓝光照射减轻了5个基因中uORF介导的mORFs的翻译抑制。借助基于数据的ORF注释，我们的分析可洞悉跨膜组以响应环境变化（例如涉及光的环境变化）。