Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, 230-0045 Yokohama, Japan.
RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, 351-0198 Wako, Japan.
Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):7831-7836. doi: 10.1073/pnas.1804971115. Epub 2018 Jun 18.
Plants adapt to alterations in light conditions by controlling their gene expression profiles. Expression of light-inducible genes is transcriptionally induced by transcription factors such as HY5. However, few detailed analyses have been carried out on the control of transcription start sites (TSSs). Of the various wavelengths of light, it is blue light (BL) that regulates physiological responses such as hypocotyl elongation and flowering time. To understand how gene expression is controlled not only by transcript abundance but also by TSS selection, we examined genome-wide TSS profiles in seedlings after exposure to BL irradiation following initial growth in the dark. Thousands of genes use multiple TSSs, and some transcripts have upstream ORFs (uORFs) that take precedence over the main ORF (mORF) encoding proteins. The uORFs often function as translation inhibitors of the mORF or as triggers of nonsense-mediated mRNA decay (NMD). Transcription from TSSs located downstream of the uORFs in 220 genes is enhanced by BL exposure. This type of regulation is found in and , major regulators of light-dependent gene expression. Translation efficiencies of the genes showing enhanced usage of these TSSs increased upon BL exposure. We also show that transcripts from TSSs upstream of uORFs in 45 of the 220 genes, including , accumulated in a mutant of NMD. These results suggest that BL controls gene expression not only by enhancing transcriptions but also by choosing the TSS, and transcripts from downstream TSSs evade uORF-mediated inhibition to ensure high expression of light-regulated genes.
植物通过控制基因表达谱来适应光照条件的变化。光诱导基因的表达由转录因子如 HY5 转录诱导。然而，对于转录起始位点（TSS）的控制，很少进行详细的分析。在各种波长的光中，蓝光（BL）调节生理反应，如下胚轴伸长和开花时间。为了了解基因表达不仅受转录丰度控制，还受 TSS 选择的控制，我们在黑暗中初始生长后，用 BL 照射处理幼苗，检查了 BL 照射后全基因组 TSS 图谱。数千个基因使用多个 TSS，一些转录物具有上游开放阅读框（uORF），优先于编码蛋白质的主 ORF（mORF）。uORF 通常作为 mORF 的翻译抑制剂或作为无意义介导的 mRNA 降解（NMD）的触发物发挥作用。在 220 个基因中的 220 个基因中，位于 uORFs 下游的 TSS 转录受到 BL 暴露的增强。这种调节类型存在于光依赖基因表达的主要调节剂 和 中。这些 TSS 增强使用的基因的翻译效率在 BL 暴露后增加。我们还表明，在包括 在内的 45 个基因中，uORFs 上游 TSS 的转录物在 NMD 突变体中积累。这些结果表明，BL 不仅通过增强转录来控制基因表达，还通过选择 TSS，并且来自下游 TSS 的转录物逃避 uORF 介导的抑制，以确保光调节基因的高表达。
