A molecular circuit integrates environmental cues to coordinate the exit from developmental dormancy

Diapause is a reversible dormancy state that enables organisms to survive extreme environments. In annual killifishes, embryos use diapause to bridge seasonal drought, but how environmental cues are integrated to trigger exit remains unclear. Here, we combine model-based single-embryo transcriptomics with cross-clade small-molecule screening to define the molecular logic of diapause exit. In the African turquoise killifish (Nothobranchius furzeri), high-resolution profiling uncovered a temporal transcriptional cascade, while transcriptomic-clock analysis revealed reduced transcriptional noise during developmental reactivation. Transcriptome-guided drug-enrichment analysis nominated overlapping compounds across two annual killifish clades, leading to a targeted chemical screen that identified shared activators and inhibitors of diapause exit. Functional assays support a model in which HSP90 integrates temperature-dependent cues with steroid-hormone signaling. Together, these findings reveal shared molecular machinery that couples environmental sensing to developmental timing, aligns diapause exit with favorable conditions, and provides a powerful comparative framework for dissecting vertebrate dormancy control.