Large-scale translatome profiling annotates functional genome and reveals the key role of genic 3ʹ untranslated regions in translatomic variation in plants

Abstract The translatome, a profile of the translational status of genetic information within cells, provides a new perspective for gene expression. Although many plant genomes have been sequenced, comprehensive translatomic annotations are not available for plants due to the lack of efficient translatome profiling techniques. Here, we developed a new technique termed 3ʹ Ribosome-profiling sequencing (3ʹRibo-seq) for reliable, robust translatomic profiling. 3ʹRibo-seq combines polysome profiling and 3ʹ 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 3ʹRibo-seq uncovered many novel translational genomic loci, thereby complementing functional genome annotation in plants. Using the low-cost, efficient 3ʹRibo-seq technique and genome-wide association mapping of translatome expression, 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 3ʹ untranslated regions of genes. Detailed eQTL analysis suggested that sequence variation around the polyA signal motif plays a key role in translatomic variation. Our study provides a comprehensive translatome annotation of plant functional genomes, and 3ʹRibo-seq that paves the way for deep translatomic analysis at the population level.