Cell Compartment-Specific Folding of Ty1 Long Terminal Repeat Retrotransposon RNA Genome

Area of Science:

• Molecular Biology
• RNA Structure
• Retrotransposition

Background:

• RNA structural dynamics during cellular trafficking remain poorly understood.
• The yeast Ty1 retrotransposon provides a model system to study these processes.
• Genome (g) RNA plays dual roles as mRNA and template for reverse transcription.

Purpose of the Study:

• To develop the first structural model of nuclear Ty1 gRNA from a retrovirus-like transposon.
• To compare nuclear Ty1 gRNA structure with cytoplasmic, virus-like particle (VLP), and in vitro synthesized structures.
• To identify structural alterations occurring during retrotransposition.

Main Methods:

• Comparative structural analysis of Ty1 gRNA in different cellular compartments and conditions.
• Prediction and modeling of RNA secondary structures.
• Investigation of RNA-RNA interactions mediated by Ty1 Gag protein.

Main Results:

• Approximately 60% of predicted base pairs in nuclear Ty1 gRNA are retained in the cytoplasm.
• Structural differences are not attributable to active translation.
• Short-range base pairings are generally conserved, while long-range pairings are compartment-specific.
• Highly structured RNA motifs are preserved during nuclear export.
• Ty1 Gag protein is crucial for RNA-RNA interactions essential for retrotransposition.

Conclusions:

• Ty1 gRNA undergoes significant structural remodeling between the nucleus and cytoplasm.
• Compartment-specific RNA structures are critical for retrotransposition.
• Ty1 Gag plays a key role in facilitating these structural rearrangements and interactions.