# Systematic discovery of subcellular RNA patterns in the gut epithelium

## TL;DR

This study maps RNA localization patterns in gut cells, revealing how RNA distribution affects intestinal function and homeostasis.

## Contribution

The work systematically identifies subcellular RNA localization patterns in gut epithelium using novel experimental techniques.

## Key findings

- Many transcripts show localization bias in granular structures within intestinal cells.
- Both intrinsic and environmental factors influence RNA localization patterns.
- Translation-dependent and -independent RNA localization mechanisms are identified.

## Abstract

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.

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.

This subcellular RNA atlas presents a detailed resource for understanding intestinal physiology.

The online version contains supplementary material available at 10.1186/s13059-025-03786-1.