Hi-C Protocol for Studying Chromatin Spatial Organization in Early Zebrafish Development

Hi-C is a high-throughput technique which allowed to discover three-dimensional chromatin structures in interphase nuclei. The questions of how these structures emerge, and how genome 3D organization can influence its function, are still poorly understood. Research in early embryos is uniquely suited to shed the light to these questions: In animal embryos, three-dimensional structures in chromatin are born during the major zygotic genome activation (ZGA) wave or shortly after it. Our own study addresses causal connection between events coinciding with ZGA and chromatin folding, using zebrafish early embryos as a model system. Here, we provide a detailed description of our Hi-C protocol adapted for zebrafish embryos.