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3plex Web: An interactive platform for RNA:DNA triplex prediction and analysis.

Marco Masera1, Chiara Cicconetti1, Francesca Ferrero1

  • 1Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Accademia Albertina 13, Torino, 10126, TO, Italy.

Computational and Structural Biotechnology Journal
|July 24, 2025
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Summary

This study introduces 3plex Web, a new platform for predicting RNA:DNA triplexes, which are crucial for long non-coding RNA (lncRNA) gene targeting. The tool offers enhanced visualization and faster analysis for exploring lncRNA functions.

Keywords:
DNAGene regulationLong non-coding RNARNARNA–DNA interactionTriplexWeb applicationlncRNA

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Long non-coding RNAs (lncRNAs) interact with DNA and proteins to regulate gene expression.
  • RNA:DNA triplexes, formed by single-stranded RNA (ssRNA) and double-stranded DNA (dsDNA), are a key mechanism for lncRNA targeting of genomic sequences.
  • Accurate prediction of these triplexes is essential for understanding lncRNA functions.

Purpose of the Study:

  • To develop an enhanced, accessible web platform (3plex Web) for predicting RNA:DNA triplexes.
  • To improve upon existing computational tools by integrating advanced features for visualization, statistical evaluation, and downstream analysis.
  • To facilitate the exploration of lncRNA regulatory mechanisms by enabling rapid and user-friendly analysis.

Main Methods:

  • Development of 3plex Web, an extension of the 3plex computational tool.
  • Integration of interactive visualization, statistical assessment with input randomization, and customizable DNA Binding Domain (DBD) selection.
  • Implementation of rapid analysis using PATO and Snakemake workflows for gene expression data integration.

Main Results:

  • 3plex Web provides enhanced prediction of RNA:DNA triplexes with improved visualization and statistical rigor.
  • The platform significantly reduces analysis processing times compared to previous methods.
  • New features enable detailed triplex stability profiling and integration with gene expression data.

Conclusions:

  • 3plex Web is a powerful and user-friendly platform for predicting RNA:DNA triplexes and studying lncRNA functions.
  • The tool accelerates research into lncRNA-mediated gene regulation.
  • Enhanced prediction capabilities will advance the understanding of molecular mechanisms involving lncRNAs.