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rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking
Jonathan L Price1, Omer Ziv1,2, Malte L Pinckert3
1Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom.
Bioinformatics (Oxford, England)
|April 10, 2024
Summary
A new R package, rnaCrosslinkOO, provides a comprehensive pipeline for analyzing in vivo RNA structural data from the COMRADES method. This tool aids in understanding RNA structure-function relationships and disease mechanisms.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genomics
Background:
- Ribonucleic acid (RNA) molecules possess complex in vivo secondary and tertiary structures vital for cellular functions, including gene expression regulation and RNA processing.
- Dysregulation of RNA structures is implicated in various diseases, highlighting the need for advanced analytical tools.
- Current methods for analyzing in vivo RNA structural data are limited, lacking mature pipelines for comprehensive processing and interpretation.
Purpose of the Study:
- To introduce rnaCrosslinkOO, a novel, object-oriented software package designed for the comprehensive analysis of in vivo RNA structural data.
- To provide a complete pipeline for processing and analyzing data generated by the Crosslinking of Matched RNA and Deep Sequencing (COMRADES) method.
- To facilitate the identification, comparison, and improved prediction of RNA structures and interactions.
Main Methods:
- Development of the rnaCrosslinkOO software package implemented in R.
- Implementation of a pipeline covering raw sequencing read processing, alignment, and duplex clustering.
- Integration of data exploration, RNA folding, structure comparison, and reactivity data incorporation.
Main Results:
- rnaCrosslinkOO offers a comprehensive workflow from raw sequencing reads to detailed RNA structural feature analysis.
- The package enables condition-based comparisons, identification of inter-RNA interactions, and enhanced structure prediction using reactivity data.
- Provides tools for exploring and comparing complex in vivo RNA structural data.
Conclusions:
- rnaCrosslinkOO addresses the need for mature pipelines in analyzing in vivo RNA structural data.
- The software enhances understanding of RNA structure-function relationships and aids in disease research.
- Facilitates advanced analysis of RNA structural dynamics and interactions.
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