Systematic identification of post-transcriptional regulatory modules

Area of Science:

• Molecular Biology
• Genomics
• Post-transcriptional Regulation

Background:

• A limited number of RNA binding proteins (RBPs) manage all RNA metabolism across the transcriptome.
• RBPs form regulatory units targeting specific RNA regulons, but their combinatorial interactions are not well understood.

Purpose of the Study:

• To systematically map RNA binding protein (RBP) combinatorial interactions using multimodal data integration.
• To generate a comprehensive map of RBP functional interactions and identify their context-specific roles.

Main Methods:

• Generated in vivo proximity-dependent biotinylation datasets for 50 human RBPs to map protein neighborhoods.
• Utilized CRISPR interference with single-cell RNA sequencing to assess transcriptomic changes after RBP knockdown.
• Integrated physical and functional interaction data with eCLIP-derived RBP mRNA targets.

Main Results:

• Created a large-scale map of RBP protein neighborhoods and functional interactions.
• Deconvoluted RBP interactions into distinct regulatory modules with annotated functions and target regulons.
• Biochemically validated predicted functions for four RBPs, demonstrating the framework's utility.

Conclusions:

• This study provides a detailed map of RBP interactions, revealing functional regulatory modules.
• The multimodal, integrative framework advances the study of post-transcriptional regulation and its mechanisms.