Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences

Area of Science:

• Molecular Biology
• Genomics
• Biochemistry

Background:

• RNA-binding proteins (RBPs) are crucial regulators of RNA metabolism, influencing processes from splicing to degradation.
• The specific RNA sequences and structures recognized by most RBPs are largely undefined, limiting our understanding of their functions.

Purpose of the Study:

• To systematically determine the RNA-binding specificities of a large collection of human RBPs.
• To identify novel roles for RBPs based on their binding preferences and to explore unconventional RNA-binding mechanisms.

Main Methods:

• Genome-scale collection of RBPs and their RNA-binding domains (RBDs).
• High-throughput RNA-selectable-element-assay (HTR-SELEX) to assess binding specificities.
• Bioinformatic analysis of motif matches in human genomic sequences and structural analysis of protein-RNA interactions.

Main Results:

• Defined binding specificities for 86 RBPs, generating 145 high-resolution models.
• Identified that ~70% of RBPs prefer linear motifs, while ~30% prefer structured motifs.
• Discovered that ZC3H12A, ZC3H12B, and ZC3H12C bind splice donor-like motifs, potentially targeting cytoplasmic viral/unspliced transcripts.
• Revealed an unconventional binding mechanism for ZC3H12B, where its RNase domain, not the C3H1 RBD, interacts with structured RNA.

Conclusions:

• This study provides the largest systematic resource of human RBP binding specificities to date.
• The findings reveal diverse RNA-binding strategies and suggest novel functions for many RBPs, including roles in RNA degradation.
• The discovery of unconventional RNA-binding mechanisms expands our understanding of how proteins interact with RNA.