Large-scale translatome profiling annotates the functional genome and reveals the key role of genic 3' untranslated regions in translatomic variation in plants.
Large-scale translatome profiling annotates the functional genome and reveals the key role of genic 3' untranslated regions in translatomic variation in plants.
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大规模翻译组分析注释了功能基因组并揭示了基因 3' 非翻译区在植物翻译组变异中的关键作用。
DOI：
10.1016/j.xplc.2021.100181
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发表时间：
2021-07-12
影响因子：
10.5
通讯作者：
Li L
中科院分区：
文献类型：
--
作者：
Zhu W;Xu J;Chen S;Chen J;Liang Y;Zhang C;Li Q;Lai J;Li L
翻译组是细胞内遗传信息翻译状态的一种模式，为基因表达提供了一个新的视角。虽然许多植物基因组已被测序，全面的翻译组注释是不可用的植物由于缺乏有效的翻译组分析技术。在这里，我们开发了一种称为3′核糖体分析测序（3′Ribo-seq）的新技术，用于可靠，强大的翻译组学分析。3 'Ribo-seq将多核糖体分析和3'选择与条形码和合并策略相结合。利用常规核糖体分析（Ribo-seq）和3′Ribo-seq对拟南芥、水稻和玉米的不同组织进行的系统性翻译组分析揭示了许多新的翻译基因组位点，从而补充了植物中的功能基因组注释。利用低成本、高效率的3′Ribo-seq技术和全基因组翻译组表达关联定位（eGWAS），对159个玉米自交系的翻译组进行了群体水平的分析，鉴定了1,777个翻译表达数量性状位点（eQTL）。值得注意的是，局部eQTL在基因的3′非翻译区显著富集。详细的eQTL分析表明，多聚腺苷酸化（polyA）信号基序周围的序列变异在翻译体变异中起着关键作用。我们的研究为植物功能基因组提供了一个全面的翻译组注释，并引入了3′Ribo-seq，这为在群体水平上进行深入的翻译组学分析铺平了道路。本研究报告了一种新的翻译组分析方法，3′Ribo-Seq，并使用常规Ribo-Seq和3′Ribo-Seq系统地注释了拟南芥、水稻和玉米的基因组，从而发现了许多新的植物功能位点。在群体水平上对翻译体表达的全基因组关联研究揭示了基因3′非翻译区在翻译体变异中的关键作用。
The translatome, a profile of the translational status of genetic information within cells, provides a new perspective on gene expression. Although many plant genomes have been sequenced, comprehensive translatomic annotations are not available for plants due to a lack of efficient translatome profiling techniques. Here, we developed a new technique termed 3′ ribosome-profiling sequencing (3′Ribo-seq) for reliable, robust translatomic profiling. 3′Ribo-seq combines polysome profiling and 3′ selection with a barcoding and pooling strategy. Systematic translatome profiling of different tissues of Arabidopsis, rice, and maize using conventional ribosome profiling (Ribo-seq) and 3′Ribo-seq revealed many novel translational genomic loci, thereby complementing functional genome annotation in plants. Using the low-cost, efficient 3′Ribo-seq technique and genome-wide association mapping of translatome expression (eGWAS), we performed a population-level dissection of the translatomes of 159 diverse maize inbred lines and identified 1,777 translational expression quantitative trait loci (eQTLs). Notably, local eQTLs are significantly enriched in the 3′ untranslated regions of genes. Detailed eQTL analysis suggested that sequence variation around the polyadenylation (polyA) signal motif plays a key role in translatomic variation. Our study provides a comprehensive translatome annotation of plant functional genomes and introduces 3′Ribo-seq, which paves the way for deep translatomic analysis at the population level. This study reports a new method, 3′Ribo-Seq, for translatome profiling and systematically annotates the genomes of Arabidopsis, rice, and maize using both conventional Ribo-seq and 3′Ribo-Seq, thereby uncovering many new functional loci in plants. A genome-wide association study of translatomic expression at the population level reveals a key role for genic 3′ untranslated regions in translatomic variation.
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作者：
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通讯作者：
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