Year: 2025
Type: article
Abstract: Long non-coding RNAs (lncRNAs) exert their functions by cooperating with other molecules, including proteins and DNA. Triplexes, formed through the interaction between a single-stranded RNA (ssRNA) and a double-stranded DNA (dsDNA), have been consistently described as a mechanism that allows lncRNAs to target specific genomic sequences in vivo. Building on the computational tool 3plex, we developed 3plex Web, an accessible platform that enhances the prediction of RNA:DNA triplexes by integrating interactive visualization, statistical evaluation, and user-friendly downstream analysis workflows. 3plex Web implements new features such as input randomization for statistical assessments, interactive profile plotting for triplex stability, and customizable DNA Binding Domain (DBD) selection. This platform enables rapid analysis through PATO, substantially reducing processing times compared to previous methods, while offering Snakemake workflows to integrate gene expression data and explore lncRNA regulatory mechanisms. Availability and implementation: 3plex Web is freely available at https://3plex.unito.it as an on-line web service. The source code for 3plex is available at https://github.com/molinerisLab/3plex, and it is paired with a definition file to setup the application in a Singularity image.
Authors: Marco Masera, Chiara Cicconetti, Francesca Ferrero, Salvatore Oliviero, Ivan Molineris
Institution: University of Turin
Language: English
Subfield: Cancer Research
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,230
OpenAlex ID: W4412440886