Chromatin architecture transitions from zebrafish sperm through early embryogenesis [ATAC-seq]
Coordinated gene expression is fundamental for cell identity, development and differentiation, and relies on a highly organized genome. Our central goal is to determine when and how higher-order 3D chromatin architecture is first established in early vertebrate embryos, its resemblance to paternal/sperm architecture, its impact on transcription, and its role in developmental transitions. We exploited the natural transition in zebrafish embryogenesis, where the zygotic genome remains transcriptionally silent until the onset of zygotic genome activation (ZGA) to assess the establishment of higher order 3D chromatin architecture by obtaining dense genome-wide Hi-C maps.  Through this approach, we defined higher-order architecture by combining advanced low-cell in-situ HiC methods with a Drosophila HiC spike-in control.  We have demonstrated the histone packed zebrafish sperm lack topological associated domains, but instead displays unique “hinge-like” domains. Prior to ZGA the zebrafish genome largely lacks physical structure, while after ZGA there are small domain-like structures detectable.  Lastly, we find initial chromatin architecture formation at super enhancers – and demonstrate that this formation is lost upon chemical inhibition of CBP/p300 activity (lowering histone H3K27ac), but not transcription inhibition. The experiments address fundamental mechanisms of initiation, how TADs are established and remodeled in vivo, and their effect on gene expression both during and after ZGA - a universal transition across animals - using the zebrafish model.  Overall design: Zebrafish sperm, and Embryos of 2.25, 4, 5.3 and 24 hours after fertilization were processed for Hi-C. ChIP-seq at 4hpf for RNA polymerase II and ATAC-seq performed at 4hpf.