Dissecting the Role of HDAC6 and HDAC8 in zebrafish

Early embryonic development requires extensive epigenetic reprogramming to enable genome activation and the establishment of developmental gene regulatory networks. Histone deacetylases (HDACs) are central regulators of chromatin and protein acetylation dynamics, yet how specific HDACs coordinate developmental reprogramming in vivo remains poorly understood. Here, we use zebrafish embryos as a vertebrate model to investigate how selective modulation of HDAC6 and HDAC8 reshapes developmental programs during early embryogenesis. Combining genetic and pharmacological perturbations with in vivo proteome and acetylome profiling, we dissect the contribution of acetylation-dependent regulation to early developmental transitions. Untargeted proteomic analysis identified over 3,000 proteins expressed during early development, while acetylome mapping revealed a restricted set of acetyl-lysine sites whose regulation is largely independent of changes in total protein abundance. Normalization of acetylation levels to corresponding protein expression uncovered site-specific acetylation events directly associated with developmental regulation rather than global proteome remodeling. Functional enrichment analyses highlighted acetylation-dependent modulation of pathways involved in cytoskeletal organization, sarcoplasmic structure, metabolism, and developmental signaling, including WNT- and Hedgehog-associated processes. Perturbation of HDAC6 and HDAC8 activity during defined developmental windows resulted in altered lineage specification, tissue organization, and morphogenetic outcomes, indicating a strong temporal dependency of acetylationbased control during genome awakening. Together, our results demonstrate that selective HDAC-mediated control of the embryonic acetylome represents a key regulatory layer of developmental reprogramming. By integrating zebrafish embryo models with quantitative proteome and acetylome analyses, we provide a systems-level view of how epigenetic regulators fine-tune genome activation and developmental trajectories in vivo.