RNAnue

RNAnue detects and analyzes RNA–RNA interactions from Direct-Duplex-Detection (DDD) data to infer intermolecular and intramolecular contacts relevant to gene regulation.

Key Features:

• Direct Duplex Detection (DDD): Employs Psoralen-mediated in vivo RNA crosslinking followed by RNA Proximity Ligation to capture interacting RNA strands.
• Sequencing Integration: Sequences crosslinked and ligated RNA molecules using classical RNA-seq to obtain reads spanning interactions.
• Specialized Bioinformatic Analysis: Implements analyses tailored for DDD data to distinguish interaction-supporting reads from standard RNA-seq signals.
• Hybridization Potential Consideration: Incorporates hybridization potential (base-pairing likelihood) into interaction prediction models.
• Statistical Significance Assessment: Applies statistical assessment to evaluate the significance and reliability of predicted RNA–RNA interactions.

Scientific Applications:

• RNA regulatory network mapping: Maps intermolecular and intramolecular RNA contacts to reconstruct RNA regulatory networks.
• Gene expression regulation studies: Identifies RNA–RNA interactions that modulate gene expression.
• RNA processing and function analysis: Characterizes RNA processing events and other cellular functions mediated by RNA molecules.

Methodology:

In vivo Psoralen crosslinking, RNA Proximity Ligation, classical RNA-seq of ligated molecules, and a specialized bioinformatics pipeline that incorporates hybridization potential and statistical significance for interaction prediction.