Systematic discovery of subcellular RNA patterns in the gut epithelium
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13059_2025_Article_3786.pdf
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Author(s)
Lee, Minkyoung
Acar, Ilhan E.
Eletto, Davide
Adivarahan, Srivathsan
Mhamedi, Farah
Handler, Kristina
Lee, Jihyun
Vinzoni, Elena G.
Aguilar, Gustavo
Date Issued
October 29, 2025
Journal
Genome Biology
Publisher
BioMed Central
Citation
Lee, M., Acar, I.E., Eletto, D. et al. Systematic discovery of subcellular RNA patterns in the gut epithelium. Genome Biol 26, 374 (2025).
Version
Final published version
Abstract
Background Subcellular RNA localization is crucial for the spatio-temporal control of protein synthesis and underlies key processes during development, homeostasis, and disease. In epithelial cells, RNA can localize asymmetrically along the apico-basal axis. Yet, the localization of most transcripts as well as the diversity of patterns that they adopt remains unexplored. Results Here, we use APEX-seq for proximity labeling and MERFISH for spatial transcriptomics to map subcellular transcript localization in intestinal organoids and tissue from adult mice. Many transcripts present localization bias, often localizing in granular structures. We uncover intrinsic and environmental factors that influence the formation of these patterns. Additionally, we identify translation-dependent and -independent localization patterns and pinpoint the role of 3′ untranslated regions and RNA-binding proteins. Conclusions This subcellular RNA atlas presents a detailed resource for understanding intestinal physiology.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Terms of Use
Creative Commons Attribution
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1186/s13059-025-03786-1
