A spatio-temporal translatome of mouse tissue development

Functional specification of mammalian tissues is a result of precise regulation of gene expression during development. Although previous transcriptomic and proteomic analyses have provided great biological insight into tissue specific gene expression and their physiological relevance in development, our understanding of translational regulation in developing tissues is lacking. Here, we report a spatio-temporally resolved translatome analysis of six mouse tissues at embryonic and adult stages to quantify the effects of translational regulation and identify new translational components. We quantified the spatial and temporal divergence of gene expression and showed specific changes in gene expression and pathways underlying the divergence. We further showed dynamic translational control by modulating translational efficiency, enhancing tissue specificity during development. We discovered thousands of actively translated upstream open read frames (ORFs) that exhibited spatio-temporal patterns and demonstrated their regulatory roles in translational regulation. Finally, we identified known and novel micropeptides encoded by small ORFs from long non-coding RNAs with functional relevance to tissue development. Our data and analyses facilitate a better understanding of complex translational regulation across tissue and developmental spectra and serve as a useful resource of mouse translatome. Overall design: Ribosome profiling (Ribo-seq) and RNA sequencing (RNA-seq) were performed for six embryo tissues and six adult tissues separately from wild-type C57BL/6 mice at embryonic day (E) 15.5 and postnatal day (P) 42, including ectoderm-derived brain and retina, mesoderm-derived heart and kidney, as well as endoderm-derived liver and lung. For each tissue, two biological replicates were performed.