Identification of new high affinity targets for Roquin based on structural conservation

Area of Science:

• Molecular Biology
• Genetics
• Bioinformatics

Background:

• Post-transcriptional gene regulation fine-tunes protein production by controlling mRNA decay and translation.
• Regulation involves trans-acting factors binding to cis-regulatory elements within mRNA untranslated regions (UTRs).
• Recognition of these elements can be sequence- or structure-based, with structural conservation indicating functional importance.

Purpose of the Study:

• To identify novel cis-regulatory elements by leveraging the evolutionary conservation of RNA structures in UTRs.
• To characterize the binding preferences and target genes of the RNA-binding protein Roquin.
• To uncover previously unknown cellular functions of Roquin.

Main Methods:

• Utilized the Dynalign RNA folding program to scan human and mouse UTRs for conserved structures.
• Characterized putative conserved structures to identify RNA-binding protein binding sites.
• Performed in vivo functional characterization to validate Roquin binding and identify new target genes.

Main Results:

• Identified previously unknown cis-regulatory elements through conserved UTR structures.
• Discovered a binding site for the RNA-binding protein Roquin.
• Redefined Roquin's binding preferences and identified numerous new target genes, many unrelated to its known roles in inflammation.
• Highlighted additional, unstudied cellular functions for Roquin.
• Found that several Roquin targets exhibit cell-type-specific expression, making them difficult to detect via mRNA abundance methods.

Conclusions:

• Evolutionary structural conservation in UTRs is a powerful strategy for discovering novel regulatory elements.
• Roquin possesses broader regulatory functions beyond immunity, impacting diverse cellular processes.
• The identified Roquin targets, especially cell-type-specific ones, represent new avenues for research into gene regulation and cellular function.