Complex biological processes such as embryogenesis require precise coordination of cell differentiation programs across both space and time. Using protein-fusion fluorescent reporters and four-dimensional live imaging, we present a protein expression atlas of transcription factors (TFs) mapped onto developmental cell lineages during Caenorhabditis elegans embryogenesis, at single-cell resolution. This atlas reveals a spatiotemporal combinatorial code of TF expression, and a cascade of lineage-specific, tissue-specific and time-specific TFs that specify developmental states. The atlas uncovers regulators of embryogenesis, including an unexpected role of a skin specifier in neurogenesis and the critical function of an uncharacterized TF in convergent muscle differentiation. At the systems level, the atlas provides an opportunity to model cell state–fate relationships, revealing a lineage-dependent state diversity within functionally related cells and a winding trajectory of developmental state progression. Collectively, this single-cell protein atlas represents a valuable resource for elucidating metazoan embryogenesis at the molecular and systems levels.

胚胎发生等复杂的生物过程需要跨空间和时间精确协调细胞分化程序。使用蛋白质融合荧光报告基因和四维实时成像，我们展示了在秀丽隐杆线虫期间映射到发育细胞谱系上的转录因子 (TF) 的蛋白质表达图谱胚胎发生，单细胞分辨率。该图谱揭示了 TF 表达的时空组合代码，以及一系列指定发育状态的谱系特异性、组织特异性和时间特异性 TF。该图谱揭示了胚胎发生的调节因子，包括皮肤特异性因子在神经发生中的意外作用以及未表征的 TF 在收敛性肌肉分化中的关键功能。在系统层面，图谱提供了模拟细胞状态-命运关系的机会，揭示了功能相关细胞内的谱系依赖性状态多样性和发展状态进展的曲折轨迹。总的来说，这个单细胞蛋白质图谱代表了在分子和系统水平上阐明后生动物胚胎发生的宝贵资源。