Spatially resolved chromatin architectures in mammalian brain tissues at cellular resolution

Unraveling the 3D chromatin architecture is crucial for decoding the regulatory program of the development and disease. However, current sequencing-based methods typically profile the 3D genome organization at the population or dissociated-cell level by sacrificing spatial context, leaving a critical gap in our understanding of how the 3D chromatin architecture changes and regulates within tissue microenvironments. Here, we present spatial Hi-C, a novel technology that resolves genome-wide chromatin structures directly within tissue sections. We demonstrated the utility of spatial Hi-C to decipher 3D chromatin structures in mouse embryos and brains with high fidelity and reproducibility. With spatial Hi-C, we revealed granular layer (GL) subclusters defined by distinct 3D genome organizations that could well aligned with specific anatomical lobules in the adult mouse cerebellum, linking chromatin topology to spatial microdomain functions. Furthermore, the spatial Hi-C of adult cortex at 10-μm resolution could reconstruct single-spot 3D chromatin structures similar to single-cell data, while capturing unique spatial contact distributions that were inaccessible to single-cell data. Remarkably, by applying spatial Hi-C to developing brains, we found an increasing radial gradient of the short-versus-long chromatin interaction ratio from the inside out on coronal sections, which could track neuronal maturity. In all, our spatial Hi-C approach establishes a powerful paradigm to investigate spatially resolved chromatin structures and their regulatory functions within complex tissue microenvironments.