Decoding RNA triple helices: identification from sequence and secondary structure.

ABSTRACT: 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 tri

SUBMITTER: Matarrese MAG 

PROVIDER: S-EPMC12834306 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature