i3plex

i3plex predicts RNA:DNA:DNA triple helix (TPX) interactions between long non-coding RNAs (lncRNAs) and genomic DNA to identify potential lncRNA binding sites and assess their thermodynamic stability.

Key Features:

• Hoogsteen pairing rules: Incorporates Hoogsteen pairing rules to constrain and score RNA:DNA:DNA triplex base-pairing.
• RNA secondary structure prediction: Predicts RNA secondary structure to account for lncRNA conformational effects on triplex formation.
• Thermal stability estimation: Assesses thermal stability of predicted TPXs using experimental thermodynamic data from published studies.
• Performance evaluation: Evaluated on re-analyzed experimental lncRNA binding-site data from human and mouse genomes, reporting comparable accuracy and reduced computational time versus other software.

Scientific Applications:

• lncRNA binding-site identification: Identification of potential genomic binding sites for lncRNAs through predicted TPXs.
• Functional characterization of lncRNAs: Inference of potential regulatory mechanisms mediated by direct lncRNA–DNA interactions via TPX formation.
• TPX discovery and characterization: Genome-wide discovery and characterization of TPXs, including the observation that TPXs can be shorter and more degenerate than previously anticipated.

Methodology:

Computational methods explicitly include application of Hoogsteen pairing rules, RNA secondary structure prediction, thermal stability assessment using experimental thermodynamic data from published studies, and evaluation against re-analyzed experimental lncRNA binding-site data from human and mouse genomes.