Unveiling Functional Long-Range RNA Structures via RIC-seq Analysis.

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• RNA conformation and structure are crucial for biological functions.
• Proximity ligation-based assays like RIC-seq capture in vivo RNA structures.
• Understanding RNA-RNA interactions requires robust computational tools.

Purpose of the Study:

• To develop and present two novel bioinformatic pipelines for analyzing RIC-seq data.
• To enable the discovery of RNA-RNA interactions using RIC-seq.
• To predict stable complementary elements within RNA structures.

Main Methods:

• Development of the RNAcontacts pipeline for extracting RNA contacts from RIC-seq data.
• Development of the PHRIC pipeline to predict complementary RNA structures based on RNA contacts.
• Implementation of both pipelines using Snakemake for reproducibility and scalability.

Main Results:

• The RNAcontacts pipeline successfully identifies RNA-RNA interactions in cis and in trans.
• The PHRIC pipeline extends RNAcontacts by predicting nested complementary elements.
• Both pipelines provide a scalable and reproducible method for analyzing transcriptomic datasets.

Conclusions:

• The developed bioinformatic pipelines offer powerful tools for RNA structure and interaction analysis.
• These tools facilitate the study of RNA conformation within physiological contexts.
• The Snakemake implementation ensures efficient and uniform processing of RIC-seq data.