Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• RNA editing, particularly adenosine to inosine (A-to-I) conversion by ADAR enzymes, is a crucial post-transcriptional modification in mammals with diverse biological roles.
• Detecting RNA editing events in large-scale transcriptome datasets remains a significant computational challenge.
• Previous analyses using REDItools have demonstrated the pervasive and specific nature of RNA editing across human tissues and cell types.

Purpose of the Study:

• To introduce REDItools, the first software package specifically designed for RNA editing profiling in RNA-sequencing (RNAseq) data.
• To present detailed bioinformatic procedures utilizing REDItools and the REDIportal database for RNA editing analysis.
• To provide protocols for investigating RNA editing in different organisms with available transcriptomic and/or genomic data.

Main Methods:

• Development of REDItools, a software package for RNA editing profiling in RNAseq data.
• Creation of REDIportal, a database containing over 4.5 million RNA editing events from large-scale human RNAseq analyses.
• Detailed description of two bioinformatic procedures: one for detecting RNA editing in a human cell line (NA12878) and another for identifying dysregulated editing in Huntington disease brain samples.

Main Results:

• REDItools has been successfully applied to human transcriptomes, revealing tissue and cell type specificity of RNA editing.
• The REDIportal database aggregates extensive RNA editing event data, facilitating further research.
• The described procedures offer a robust workflow for RNA editing detection and analysis in various biological samples and organisms.

Conclusions:

• REDItools and REDIportal provide essential computational resources for the comprehensive study of RNA editing.
• The developed bioinformatic procedures enable detailed investigation of RNA editing patterns and their alterations in disease contexts.
• These tools and protocols are designed for broad applicability across different species with available sequencing data.