RNA-DNA triplexes: molecular mechanisms and functional relevance

Hoogsteen base pairing enables the association of an RNA strand with a DNA double-helix, allowing the formation of RNA-DNA triplexes, which now have been identified to occur in vivo.Such identifications require specific bioinformatic, biochemical, and biophysical methods, offering experimental opportunities, but also render the field complex.Triplex formation has been best studied for long non-coding RNAs (lncRNAs).Numerous lncRNAs fine-tune gene expression through triplex formation.Many aspects of triplex biology still await clarification, making this research field highly dynamic. Interactions of RNA with DNA are principles of gene expression control that have recently gained considerable attention. Among RNA–DNA interactions are R-loops and RNA-DNA hybrid G-quadruplexes, as well as RNA-DNA triplexes. It is proposed that RNA-DNA triplexes guide RNA-associated regulatory proteins to specific genomic locations, influencing transcription and epigenetic decision making. Although triplex formation initially was considered solely an in vitro event, recent progress in computational, biochemical, and biophysical methods support in vivo functionality with relevance for gene expression control. Here, we review the central methodology and biology of triplexes, outline paradigms required for triplex function, and provide examples of physiologically important triplex-forming long non-coding RNAs. Interactions of RNA with DNA are principles of gene expression control that have recently gained considerable attention. Among RNA–DNA interactions are R-loops and RNA-DNA hybrid G-quadruplexes, as well as RNA-DNA triplexes. It is proposed that RNA-DNA triplexes guide RNA-associated regulatory proteins to specific genomic locations, influencing transcription and epigenetic decision making. Although triplex formation initially was considered solely an in vitro event, recent progress in computational, biochemical, and biophysical methods support in vivo functionality with relevance for gene expression control. Here, we review the central methodology and biology of triplexes, outline paradigms required for triplex function, and provide examples of physiologically important triplex-forming long non-coding RNAs.