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Background <p>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.</p> Results <p>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.</p> Conclusions <p>This subcellular RNA atlas presents a detailed resource for understanding intestinal physiology.</p>

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Systematic discovery of subcellular RNA patterns in the gut epithelium

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年10月29日

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  • Minkyoung Lee,
  • Ilhan E. Acar,
  • Davide Eletto,
  • Srivathsan Adivarahan,
  • Farah Mhamedi,
  • Kristina Handler,
  • Jihyun Lee,
  • Elena Guido Vinzoni,
  • Gustavo Aguilar,
  • Andreas E. Moor

摘要

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.