Precise detection of differential RNA editing sites across varied biological conditions using the CADRES pipeline

Abstract

Abstract RNA editing is an important post-transcriptional modification for gene regulation and protein diversity. Detecting these modifications, especially Differential Variants on RNA (DVRs), presents significant challenges due to interference from sequencing errors and genetic variants. Currently, despite millions of A>I editing sites having been identified, a significant gap remains in identifying C>U RNA editing sites, mediated by cytidine deaminases, which target both DNA and RNA. To improve the detection and analysis of C>U RNA editing sites, we developed the Calibrated Differential RNA Editing Scanner (CADRES), an analytical pipeline that combines sophisticated DNA/RNA variant calling with detailed statistical analysis on depth of RNA editing. This study validates CADRES through rigorous in silico and experimental datasets using inducible cell models of the APOBEC3B (A3B) deaminase. CADRES demonstrates improved specificity and accuracy over existing methodologies, effectively identifying A3B-mediated C>U edits while filtering against sequencing artefacts and A3B-mediated DNA mutations. Our findings demonstrate that CADRES provides a reliable tool for the precise identification of C>U RNA editing sites, which will help understand the molecular mechanisms underlying cytidine deamination on RNA and its functions.

Keywords

• RNA editing
• Next-generation sequencing
• Differential Variants on RNA (DVRs)
• Bioinformatics
• Variant calling
• APOBEC deaminase