Dissection of context-dependent RNA colocalization landscapes from subcellular spatial transcriptomics data

Post-transcriptional RNA processes, including translation, decay, and modification, depend critically on the coordinated spatial organization of RNA molecules. Leveraging densely sampled intracellular RNA distributions from high-resolution spatial transcriptomics (ST), we developed the Subcellular Colocalized RNA Interaction Network (SCRIN) analysis, a computational framework that uses hypergeometric testing to systematically quantify local enrichment of different RNA species. SCRIN robustly reconstructs cell- and tissue-specific RNA colocalization landscapes with high precision. These context-dependent RNA colocalization networks are closely associated with gene functions and biological processes traditionally studied at the protein level. We show that RNA colocalization patterns dynamically reorganize during tissue development and adaptively rewire upon physiological perturbations, representing a widespread and tightly regulated layer of post-transcriptional control. Collectively, our results establish spatiotemporally coordinated RNA interactions as a biologically influential yet underexplored regulatory layer, a significant extension beyond the well-studied protein interaction networks. SCRIN thus opens a new avenue and provides an unprecedented resource for dissecting the functional and mechanistic roles of subcellular transcriptome organization in complex biological processes.