FLARE: a Fast and Flexible Workflow for Identifying RNA Editing Foci

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2023 Oct 2

PMID 37784060

Authors

Eric Kofman

Brian Yee

Hugo C Medina-Munoz

Gene W Yeo

Affiliations

Soon will be listed here.

Abstract

Background: Fusion of RNA-binding proteins (RBPs) to RNA base-editing enzymes (such as APOBEC1 or ADAR) has emerged as a powerful tool for the discovery of RBP binding sites. However, current methods that analyze sequencing data from RNA-base editing experiments are vulnerable to false positives due to off-target editing, genetic variation and sequencing errors.

Results: We present FLagging Areas of RNA-editing Enrichment (FLARE), a Snakemake-based pipeline that builds on the outputs of the SAILOR edit site discovery tool to identify regions statistically enriched for RNA editing. FLARE can be configured to analyze any type of RNA editing, including C to U and A to I. We applied FLARE to C-to-U editing data from a RBFOX2-APOBEC1 STAMP experiment, to show that our approach attains high specificity for detecting RBFOX2 binding sites. We also applied FLARE to detect regions of exogenously introduced as well as endogenous A-to-I editing.

Conclusions: FLARE is a fast and flexible workflow that identifies significantly edited regions from RNA-seq data. The FLARE codebase is available at https://github.com/YeoLab/FLARE .

Citing Articles

ncRNA Editing: Functional Characterization and Computational Resources.

Marceca G, Romano G, Acunzo M, Nigita G Methods Mol Biol. 2024; 2883:455-495.

PMID: 39702721 DOI: 10.1007/978-1-0716-4290-0_20.

LoDEI: a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data.

Torkler P, Sauer M, Schwartz U, Corbacioglu S, Sommer G, Heise T Nat Commun. 2024; 15(1):9121.

PMID: 39443485 PMC: 11500352. DOI: 10.1038/s41467-024-53298-y.

High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.

Liang Q, Yu T, Kofman E, Jagannatha P, Rhine K, Yee B Nat Commun. 2024; 15(1):7067.

PMID: 39152130 PMC: 11329496. DOI: 10.1038/s41467-024-50363-4.

A-to-I Editing Is Subtype-Specific in Non-Hodgkin Lymphomas.

Chen C, Bundschuh R Genes (Basel). 2024; 15(7).

PMID: 39062643 PMC: 11276283. DOI: 10.3390/genes15070864.

Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.

Medina-Munoz H, Kofman E, Jagannatha P, Boyle E, Yu T, Jones K Nat Commun. 2024; 15(1):875.

PMID: 38287010 PMC: 10825223. DOI: 10.1038/s41467-024-45009-4.

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