Subcellular spatial transcriptomics identifies three mechanistically different classes of localizing RNAs

Area of Science:

• Cell Biology
• Molecular Biology
• Genetics

Background:

• Intracellular RNA localization is crucial for cell polarization and gene expression.
• Existing studies on RNA localization mechanisms in Drosophila are limited in scope and tissue-specific analysis.
• A comprehensive understanding of RNA localization within a single tissue type is lacking.

Purpose of the Study:

• To identify and mechanistically analyze RNAs localized to apical and basal domains in the columnar follicular epithelium (FE).
• To elucidate the motor protein-dependent mechanisms governing RNA transport in FE cells.

Main Methods:

• Subcellular spatial transcriptomics was employed to map RNA distribution.
• Mechanistic investigations focused on the roles of dynein, kinesin-1, BicD, and Egl in RNA transport.
• Analysis included a non-canonical, translation- and dynein-dependent pathway.

Main Results:

• Identified distinct sets of RNAs localized to apical and basal domains of FE cells.
• Dynein/BicD/Egl machinery mediates apical RNA localization.
• Kinesin-1 is required for basally-targeted RNAs to counteract default dynein-mediated transport.
• A novel mechanism involving translation and dynein drives apical localization of specific adaptor-encoding RNAs.

Conclusions:

• At least three distinct mechanisms control RNA localization in the FE.
• RNA localization is linked to the formation of dynein/dynactin/adaptor complexes in vivo.
• This work provides a comprehensive mechanistic view of RNA localization within a single tissue.