Sequence grammar and dynamics of subcellular translation revealed by APEX-Ribo-Seq

Local translation at specific subcellular regions is proposed to define appropriate protein destinations and functions. However, our understanding of local translation is still far from complete, due to a lack of versatile analysis tools. Here, we developed a new method, termed “APEX-Ribo-Seq”, that integrates ribosome profiling (Ribo-Seq) with APEX2-based proximity labeling. We mapped local translation at 14 distinct organelles and identified over 3000 genes that are locally translated. Interpretable machine learning methods based on RNA language models systematically uncovered RNA-binding proteins with key roles in compartment-specific translation. In addition, we revealed slow translation kinetics associated with cotranslational membrane insertion of nascent chains. APEX-Ribo-Seq also captured cell cycle-regulated dynamics at the centrosome and stress-regulated programs at stress granules and autophagosomes. We also demonstrated the utility of APEX-Ribo-Seq in primary neurons, revealing compartment-specific translatomes in dendrites, axons, and presynapses. Our results provide a comprehensive view of the spatiotemporal translatome and its regulation.