Comprehensive Identification of RNA-Binding Domains in Human Cells

Area of Science:

• Molecular Biology
• Proteomics
• Genomics

Background:

• Mammalian cells contain over a thousand RNA-binding proteins (RBPs).
• Approximately half of these RBPs utilize unknown RNA-binding mechanisms.
• Understanding protein-RNA interactions is crucial for cellular function.

Purpose of the Study:

• To develop and apply a proteome-wide method for identifying RNA-binding sites on native RBPs.
• To investigate the relationship between RNA-binding sites and other protein domains.
• To explore the functional and evolutionary significance of identified RNA-binding sites.

Main Methods:

• Development of RBDmap, a novel technique for mapping RNA-binding sites.
• Application of RBDmap to HeLa cell proteome for large-scale RBP analysis.
• Bioinformatic analysis of identified RNA-binding domains (RBDs) and their associated protein features.

Main Results:

• Identified 1,174 RNA-binding sites across 529 RBPs in HeLa cells.
• Discovered numerous novel RNA-binding domains (RBDs).
• Found RNA-binding sites are frequently located near catalytic or protein-protein interaction domains, and within intrinsically disordered regions.
• Observed RNA-binding sites are hotspots for post-translational modifications like acetylation and phosphorylation.
• Demonstrated high evolutionary conservation and incidence of Mendelian mutations in RBDs.

Conclusions:

• RBDmap provides a powerful tool for studying native protein-RNA interactions at a proteome-wide scale.
• RNA binding is intricately linked to protein function, regulation, and evolution.
• Intrinsically disordered regions play a significant role in protein-RNA interactions.
• Post-translational modifications suggest dynamic regulation of RBP activity.