Spatially resolved chromatin architectures in mammalian brain tissues

Unraveling 3D chromatin architectures is crucial for decoding regulatory programs of development and disease. However, current sequencing-based methods typically profile 3D genome organizations while sacrificing the spatial context of tissues. Here we present spatial high‑throughput chromosome conformation capture (Hi-C), a technology that resolves genome-wide chromatin structures directly within tissue sections. Spatial Hi-C could decipher 3D chromatin structures in mouse embryos and brains with high fidelity and reproducibility. In the cerebellum, granular layer subclusters defined by distinct 3D genomes, aligned with anatomical lobules, link chromatin topology to spatial microdomain functions. Furthermore, spatial Hi-C of the adult cortex could reconstruct single-spot 3D chromatin structures at 10-μm resolution, similar to single-cell data. Finally, we found an increasing radial gradient of the short-versus-long chromatin interaction ratio on coronal sections in developing brains, which could track neuronal maturity. In summary, spatial Hi-C establishes a paradigm to investigate spatially resolved chromatin structures and their regulatory functions within complex tissue microenvironments.