Work

Ψ-co-mAFiA: concurrent detection of pseudouridine and m6A in single RNA molecules

Year: 2025

Type: article

Abstract: SUMMARY: The development of third-generation sequencing technologies enables the detection of RNA modifications at single-molecule resolution. Specifically for direct RNA sequencing on the ONT platform, we have previously developed an m6A detection algorithm called mAFiA. Here, we present the updated method, now covering all 18 DRACH m6A contexts as well as the identification of pseudouridine sites (Ψ). Our modification level predictions compare favorably with orthogonal methods and respond to knockdown or knock out of writer proteins. The simultaneous detection of multiple modifications on a single RNA molecule opens up the possibility to study cross-modification interactions. AVAILABILITY AND IMPLEMENTATION: Ψ-co-mAFiA is available at https://github.com/dieterich-lab/psi-co-mAFiA and licensed under GPLv3.0. An archived version of the software is available on Zenodo at https://doi.org/10.5281/zenodo.16797676.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btaf536

Authors: Adrian Chan, Isabel S Naarmann-de Vries, Christoph Dieterich

Institutions: University Hospital Heidelberg, German Centre for Cardiovascular Research

Language: English

Topic: RNA modifications and cancer

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,989

Funder: Klaus Tschira Stiftung