Environmental adaptation often involves changes in gene regulation, but it remains unclear when such regulatory divergence emerges during vertebrate development, how much is maternally inherited, and how it relates to evolutionary constraint in cis-regulatory landscapes. CaveAGE addresses this question in the Mexican tetra, Astyanax mexicanus, an EvoDevo model in which cave and surface morphs differ in pigmentation, eye development, behaviour and metabolism, while remaining interfertile.CaveAGE will determine when and how regulatory divergence appears during early Astyanax embryogenesis, and whether changes in promoter usage, transcription initiation and enhancer-associated transcription precede overt morphological divergence. We will generate a stage-resolved CAGE atlas of cave, surface and reciprocal hybrid embryos across four developmental windows spanning the maternal-to-zygotic transition, zygotic genome activation and later embryogenesis. CAGE will map transcription start sites, promoter activity, alternative promoter usage and enhancer-associated transcription at base-pair resolution. Reciprocal hybrids will distinguish maternally inherited regulatory programs from zygotic effects, while comparative analyses of conserved non-coding elements and genomic regulatory blocks will place divergent regulatory elements in evolutionary context. Genomic language models will provide sequence-level hypotheses, and selected candidates will be validated by promoter-specific RT-qPCR and in situ hybridisation.The project will deliver the first developmental transcription-initiation atlas for Astyanax, open promoter/enhancer annotations, comparative conservation maps, prioritised regulatory candidates and reproducible workflows. By linking developmental timing, inheritance and cis-regulatory architecture, CaveAGE will advance understanding of how environmental adaptation reshapes vertebrate developmental gene regulation.