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Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics
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DOI：10.1038/s41467-026-72156-7.png)
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Abstract
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Subcellular RNA localization, including nuclear retention and apical-basal compartmentalization in polarized epithelia plays a central role in post-transcriptional regulation. However, methods for high-throughput mapping of mRNA localization within intact tissue sections remain limited. Here, we apply high-resolution spatial transcriptomics to systematically resolve intracellular mRNA localization across diverse mammalian tissues. We introduce a computational approach that leverages image-derived features to extract subcellular information from spatial data and quantifies transcript localization patterns. Using this framework, we map apical-basal mRNA localization and nuclear retention in gastrointestinal epithelia and in liver hepatocytes. Our analyses reveal conserved and tissue-specific localization signatures. This approach broadens the scope of spatial transcriptomics by enabling routine investigation of intracellular RNA distributions in both healthy and diseased tissues. Subcellular RNA localization plays a central role in post-transcriptional regulation. Using high-resolution spatial transcriptomics and a computational approach, the study maps intracellular mRNA localization across tissues, revealing conserved localization patterns and enabling routine analysis of RNA distribution in cells.
Keywords:
Apicobasal polarity
Computational biology and bioinformatics
RNA transport
Systems biology
Science
Humanities and Social Sciences
multidisciplinary
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