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. 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.哺乳动物组织的功能特化，是发育过程中基因表达精准调控的产物。尽管此前的转录组学（transcriptomic）与蛋白质组学（proteomic）分析已为组织特异性基因表达及其在发育中的生理相关性提供了重要生物学见解，但我们对发育中组织的翻译调控机制仍缺乏充分认知。本研究针对胚胎期与成年期的6种小鼠组织开展时空解析翻译组（translatome）分析，以量化翻译调控的效应并鉴定全新的翻译调控组分。我们量化了基因表达的时空差异，并揭示了该差异背后特定的基因表达与通路变化。我们进一步证实，发育进程中通过调控翻译效率可实现动态翻译调控，进而强化组织特异性表达。我们发现了数千个呈现时空表达模式的活跃翻译上游开放阅读框（upstream open read frames, ORFs），并证实其在翻译调控中发挥调控功能。最后，我们从长链非编码RNA（long non-coding RNAs）的小开放阅读框中鉴定出已知与新型微肽，且这些微肽与组织发育功能密切相关。本研究产生的数据与分析结果，有助于我们更深入理解跨组织与发育谱系的复杂翻译调控机制，同时可作为小鼠翻译组的宝贵研究资源。本研究针对野生型C57BL/6小鼠的胚胎期（胚胎第15.5天，E15.5）与成年期（出生后第42天，P42）的6种胚胎组织与6种成年组织，分别开展了核糖体谱分析（Ribosome profiling, Ribo-seq）与RNA测序（RNA sequencing, RNA-seq），所涉组织包括外胚层来源的脑与视网膜、中胚层来源的心脏与肾脏，以及内胚层来源的肝脏与肺脏。每种组织均设置2次生物学重复。