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.
Show 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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