RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Non-coding RNA (ncRNA) interactions are fundamental to gene regulation.
• Identifying RNA-RNA interactions is key for understanding ncRNA functions.
• Sequence complementarity is a strong indicator of RNA-RNA interactions.

Purpose of the Study:

• To introduce RIsearch2, a tool for large-scale RNA-RNA interaction prediction.
• To develop an siRNA off-target discovery pipeline.
• To enable efficient and accurate prediction of RNA interactions and siRNA off-target effects.

Main Methods:

• Developed RIsearch2 using a novel seed-and-extend framework based on suffix arrays.
• Integrated genome-wide predictions with target site accessibility and transcript abundance for siRNA off-target analysis.
• Utilized near-complementarity as a primary prediction criterion.

Main Results:

• RIsearch2 enables rapid identification of potential RNA-RNA interactions on a genome-wide scale.
• The siRNA off-target discovery pipeline accurately predicts off-target transcripts.
• The pipeline effectively computes siRNA off-targeting potential and allows comparisons between designs.

Conclusions:

• RIsearch2 provides a fast and scalable method for discovering RNA-RNA interactions.
• The integrated pipeline enhances the prediction accuracy of siRNA off-target effects.
• These tools are valuable for functional ncRNA studies and siRNA design optimization.