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bioRxiv · 10.1101/2025.09.07.674688

Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics

Novoselsky, R.·Golani, O.·Barkai, T.·Kedmi, M.·Goliand, I.·Fine, M.·Kent, I.·Nachmany, I.·Itzkovitz, S.
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Abstract

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 (VisiumHD) to systematically resolve intracellular mRNA localization across diverse mammalian tissues. We introduce a computational approach that extracts subcellular features 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 that can be readily obtained from standard high-definition spatial transcriptomics experiments. This approach broadens the scope of spatial transcriptomics by enabling routine investigation of intracellular RNA distributions in both healthy and diseased tissues.

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Novoselsky, R., Golani, O., Barkai, T., Kedmi, M., Goliand, I., Fine, M., Kent, I., Nachmany, I., Itzkovitz, S.. 2025-09-09. Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics. https://doi.org/10.1101/2025.09.07.674688

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