Genome-wide chromatin accessibility during early embryogenesis in a generalist cichlid fish

Abstract

Background Lake Malawi's haplochromine cichlids are one of the most rapid and species-rich vertebrate adaptive radiations known, generating hundreds of species within < 1 million years, yet how regulatory regions shape their embryonic development remains poorly understood. Astatotilapia calliptera, a generalist riverine lineage and proxy for the ancestral stock that seeded this radiation, offers a developmental chromatin baseline against which regulatory divergence in specialised lineages can be compared. Results We generated genome-wide ATAC-seq profiles of A. calliptera embryos across three developmental stages (3, 7 and 12 days post-fertilisation, dpf), identifying 550,876-701,889 accessible chromatin peaks per stage. Accessible chromatin was enriched at gene promoters and at both highly conserved and accelerated conserved noncoding elements at every stage. The functional repertoire of accessible-promoter genes shifted across development, from early patterning at 3 dpf to the broadest regulatory repertoire at 7 dpf, and an increasingly neural- and locomotory-behaviour-enriched repertoire by 12 dpf, coinciding with post-hatching motor maturation. Differential accessibility showed that chromatin opening, rather than closing, dominates the earliest transitions (3 vs 7 and 3 vs 12 dpf), driven mostly by general metabolic genes, whereas the smaller, later 7 vs 12 dpf transition combined targeted gains at tissue-remodelling and apoptosis genes with losses at genes governing early neural and retinal patterning; almost all of these losses (96%) were at promoters that had opened between 3 and 7 dpf, indicating transient rather than sustained opening. Transcription factor (TF) footprinting identified stage-specific regulatory activity among developmentally important TFs, while the broader TF-promoter network remained topologically stable across all three stages, built around conserved hub regulators of core neural and sensory patterning genes e.g., SOX2, FOXG1, PTF1A, SOX10. This suggests that wiring is established early and largely maintained, following the hourglass model, with developmental progression driven by changes in activity of this conserved programme. Conclusions Together, these findings establish the first embryonic epigenomic resource for A. calliptera, revealing a developmental chromatin landscape of broad early opening and progressive functional specialisation, and providing a comparative framework for understanding how regulatory evolution has shaped Lake Malawi cichlid diversification.