Integrative spatial profiling of 3D genome organization and gene expression in tissue.

Spatial Hi-C-RNA simultaneously maps genome-wide chromatin contacts and transcriptomes from the same intact tissue section at near-single-cell resolution, revealing complementary spatial patterns in mouse brain, embryos, and human melanoma.

• Why it matters: Measuring how 3D genome organization coordinates transcription in situ is difficult, limiting understanding of genome structure–function relationships during development and across tumor states.
• What they did: The multimodal platform integrates chromatin and RNA profiling from the same tissue section, generating multimodal maps across mouse brain, developing embryos, and human melanoma.
• The result: Chromatin features (A/B compartments, topologically associating domains, and loops) are linked to region- and cell-type-specific transcriptional programs, resolving neuronal maturation remodeling in mouse embryos and intratumoral subregions and tumor-state transitions in human melanoma.

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