RNA:DNA triple helices: from peculiar structures to pervasive chromatin regulators

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• Complex eukaryotes possess extensive non-protein-coding DNA transcribed into non-coding RNAs (ncRNAs).
• ncRNAs play vital roles in chromatin regulation, often by recruiting chromatin modifiers.
• Understanding how ncRNAs bind to specific DNA targets is crucial but remains challenging.

Purpose of the Study:

• To review current knowledge on RNA:DNA triplexes, including their formation, detection, and associated ncRNAs.
• To highlight the growing evidence for RNA:DNA triplexes as a significant mode of ncRNA-chromatin interaction.

Main Methods:

• Review of existing literature on RNA:DNA triplexes.
• Summary of triplex formation rules and detection methodologies.
• Analysis of recent high-throughput and computational studies.

Main Results:

• RNA:DNA triplexes, alongside R-loops, represent a key mechanism for direct RNA-DNA interactions.
• While functional characterization is ongoing, evidence suggests widespread genomic distribution of RNA:DNA triplexes.
• Recent advances indicate a paradigm shift in understanding these structures.

Conclusions:

• RNA:DNA triplexes are emerging as a prominent mechanism for ncRNA-mediated chromatin regulation.
• Further research is needed to fully elucidate the functional roles of these interactions.