biostudies-literatureUnknown27(1)Matarrese MAGEuropean Union - NextGeneration EU - National Recovery and Resilience Plan (NRRP)European Union – NextGeneration EU – National Recovery and Resilience PlanThe discovery of long non-coding RNAs (lncRNA) has revealed additional layers of gene-expression control. Specific interactions of lncRNAs with DNA, RNAs, and RNA-binding proteins enable regulation in both cytoplasmic and nuclear compartments; e.g. a conserved triple-helix motif is essential for MALAT1 stability and oncogenic activity. Here, we present a secondary-structure-based framework to annotate and detect RNA triple helices. First, we extend the dot-bracket formalism with a third annotation line that encodes Hoogsteen contacts. Second, we introduce TripleMatcher, which searches for a triple-helix pattern, filters candidates by C1'-C1' distance thresholds, and merges overlaps into region-level zones. Using telomerase RNAs and RNA-stability elements with experimentally established triBriefings in bioinformaticsbbag009https://www.ebi.ac.uk/biostudies/studies/S-EPMC12834306biostudies-literatureDecoding RNA triple helices: identification from sequence and secondary structure.PMC12834306Ballarino MLuchetti NDurante DMatarrese MAGDi Petta FTesei LChiodo LQuadrini MfalseDecoding RNA triple helices: identification from sequence and secondary structure.The discovery of long non-coding RNAs (lncRNA) has revealed additional layers of gene-expression control. Specific interactions of lncRNAs with DNA, RNAs, and RNA-binding proteins enable regulation in both cytoplasmic and nuclear compartments; e.g. a conserved triple-helix motif is essential for MALAT1 stability and oncogenic activity. Here, we present a secondary-structure-based framework to annotate and detect RNA triple helices. First, we extend the dot-bracket formalism with a third annotation line that encodes Hoogsteen contacts. Second, we introduce TripleMatcher, which searches for a triple-helix pattern, filters candidates by C1'-C1' distance thresholds, and merges overlaps into region-level zones. Using telomerase RNAs and RNA-stability elements with experimentally established tri2026-01-01T00:00:00Z2026 Jan2026-06-15T08:49:17.998Z2026-06-15T03:11:29.802ZS-EPMC128343064158732110.1093/bib/bbag009