Pre-ZGA 3D genome architecture emerges modularly in Drosophila embryos

Using Pico-C, a low-input Micro-C method, the study maps high-resolution 3D genome architecture across NC9–NC14 in early Drosophila embryos and reveals that chromatin loops and boundaries emerge in an ordered, modular fashion before major ZGA. Transcriptional elongation inhibition preserves some early loops but weakens promoter insulation, while sequence-based models show orthogonal motif-driven contributions to architecture. Co-depleting Zelda and GAF confirms locus-specific regulatory inputs, supporting a layered regulatory logic for genome establishment prior to ZGA.