FLARE

FLARE identifies regions statistically enriched for RNA editing (A-to-I and C-to-U) to map RNA-binding protein (RBP) interactions and detect endogenous or exogenous editing events.

Key Features:

• Versatility in RNA editing types: Supports analysis of C-to-U and A-to-I RNA editing.
• Integration with SAILOR outputs: Leverages outputs from the SAILOR edit site discovery tool to pinpoint regions enriched for editing.
• High specificity in detection: Demonstrated high specificity for detecting RBP binding sites, including application to C-to-U data from an RBFOX2-APOBEC1 STAMP experiment.
• Application to endogenous and exogenous editing: Applicable to detection of both exogenously introduced and endogenous A-to-I editing events.
• Workflow implementation: Implemented as a Snakemake-based, fast and flexible workflow for processing RNA-seq from RNA-base editing experiments.

Scientific Applications:

• Mapping RBP interactions: Identification of RBP binding sites using fusions of RBPs to base-editing enzymes such as APOBEC1 or ADAR.
• Studying RNA-editing–mediated regulation: Analysis of enriched editing regions to investigate gene regulation mechanisms mediated by RNA editing.

Methodology:

Snakemake-based pipeline that ingests RNA-seq from RNA-base editing experiments and SAILOR edit site outputs, applies statistical methods to identify regions with significant enrichment for RNA editing, and reduces false positives from off-target editing, genetic variation, and sequencing errors.