RNA structure-wide discovery of functional interactions with multiplexed RNA motif library

Area of Science:

• Molecular Biology
• Genomics
• Biochemistry

Background:

• RNA structures are prevalent in transcripts but their functions remain largely unknown.
• Understanding RNA structure-function relationships is crucial for deciphering cellular processes.

Purpose of the Study:

• To develop a high-throughput method for identifying functional RNA structures and their interactions.
• To investigate the roles of RNA structures in RNA-protein interactions and gene regulation.

Main Methods:

• Developed Folded RNA Element Profiling with Structure Library (FOREST), a multiplexed affinity assay.
• Created an RNA structure library from validated or predicted RNA motifs.
• Applied FOREST to transcriptome-wide RNA structure datasets for high-throughput analysis.

Main Results:

• FOREST identified multiple RNA-protein interaction networks with quantitative scores.
• Discovered translational regulatory elements functioning in living cells.
• Revealed distinct binding landscapes for RNA G-quadruplex (rG4) structure-binding proteins and identified novel rG4 structures in precursor microRNAs.

Conclusions:

• FOREST is a versatile platform for large-scale investigation of RNA structure-function relationships.
• The method enables comprehensive identification of functional RNA elements and their interactors.
• Findings advance the understanding of RNA-mediated regulation and molecular mechanisms.