National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
Plant Commun. 2023 Mar 13;4(2):100457. doi: 10.1016/j.xplc.2022.100457. Epub 2022 Oct 4.
Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from mRNAs. Many studies have revealed translational regulation in plants in response to various environmental stimuli. However, there have been no studies documenting the comprehensive landscape of translational regulation and allele-specific translational efficiency in multiple plant tissues, especially those of rice, a main staple crop that feeds nearly half of the world's population. Here we used RNA sequencing and ribosome profiling data to analyze the transcriptome and translatome of an elite hybrid rice, Shanyou 63 (SY63), and its parental varieties Zhenshan 97 and Minghui 63. The results revealed that gene expression patterns varied more among tissues than among varieties at the transcriptional and translational levels. We identified 3392 upstream open reading frames (uORFs), and the uORF-containing genes were enriched in transcription factors. Only 668 of 13 492 long non-coding RNAs could be translated into peptides. Finally, we discovered numerous genes with allele-specific translational efficiency in SY63 and demonstrated that some cis-regulatory elements may contribute to allelic divergence in translational efficiency. Overall, these findings may improve our understanding of translational regulation in rice and provide information for molecular breeding research.
翻译调控是基因表达过程中的一个关键步骤，它控制着从 mRNA 合成蛋白质的过程。许多研究已经揭示了植物对各种环境刺激的翻译调控。然而，目前还没有研究记录在多个植物组织中，特别是在水稻（一种主要的主食作物，养活了世界近一半的人口）中，翻译调控和等位基因特异性翻译效率的综合情况。在这里，我们使用 RNA 测序和核糖体分析数据来分析一个优良杂交水稻品种汕优 63（SY63）及其亲本品种珍汕 97 和明恢 63 的转录组和翻译组。结果表明，在转录和翻译水平上，基因表达模式在组织间的变化大于品种间的变化。我们鉴定了 3392 个上游开放阅读框（uORFs），包含 uORF 的基因富集在转录因子中。在 13492 个长非编码 RNA 中，只有 668 个能够翻译成肽。最后，我们在 SY63 中发现了许多具有等位基因特异性翻译效率的基因，并表明一些顺式调控元件可能导致翻译效率的等位基因分化。总的来说，这些发现可能有助于我们理解水稻中的翻译调控，并为分子育种研究提供信息。
