Systematic discovery of subcellular RNA patterns in the gut epithelium

Area of Science:

• Molecular Biology
• Cell Biology
• Genomics

Background:

• Subcellular RNA localization is vital for controlling protein synthesis spatially and temporally.
• Epithelial cells exhibit apico-basal RNA asymmetry, but most transcript patterns remain unknown.
• Understanding RNA localization is critical for development, homeostasis, and disease processes.

Purpose of the Study:

• To map the subcellular localization of transcripts in intestinal organoids and tissues.
• To identify factors influencing RNA pattern formation.
• To characterize translation-dependent and -independent localization mechanisms.

Main Methods:

• Utilized APEX-seq for proximity labeling to identify RNA-protein interactions.
• Employed MERFISH (Multiplexed Fluorescence In Situ Hybridization) for spatial transcriptomics.
• Analyzed transcript localization patterns in adult mouse intestinal organoids and tissue.

Main Results:

• Discovered that numerous transcripts exhibit biased subcellular localization, often within granular structures.
• Identified intrinsic and environmental factors that regulate the formation of these RNA localization patterns.
• Differentiated between translation-dependent and -independent localization, highlighting the roles of 3' UTRs and RNA-binding proteins.

Conclusions:

• Developed a comprehensive subcellular RNA atlas for the mouse intestine.
• This atlas serves as a valuable resource for advancing the understanding of intestinal physiology.
• The findings provide insights into the complex regulation of RNA localization in epithelial cells.