The RMaP challenge of predicting RNA modifications by nanopore sequencing

The field of epitranscriptomics is undergoing a technology-driven revolution. During past decades, RNA modifications like N6-methyladenosine (m<sup>6</sup>A), pseudouridine (ψ), and 5-methylcytosine (m<sup>5</sup>C) became acknowledged for playing critical roles in cellular processes. Direct RNA sequencing by Oxford Nanopore Technologies (ONT) enabled the detection of modifications in native RNA, by detecting noncanonical RNA nucleosides properties in raw data. Consequently, the field's cutting edge has a heavy component in computer science, opening new avenues of cooperation across the community, as exchanging data is as impactful as exchanging samples. Therefore, we seize the occasion to bring scientists together within the RNA Modification and Processing (RMaP) challenge to advance solutions for RNA modification detection and discuss ideas, problems and approaches. We show several computational methods to detect the most researched mRNA modifications (m<sup>6</sup>A, ψ, and m<sup>5</sup>C). Results demonstrate that a low prediction error and a high prediction accuracy can be achieved on these modifications across different approaches and algorithms. The RMaP challenge marks a substantial step towards improving algorithms' comparability, reliability, and consistency in RNA modification prediction. It points out the deficits in this young field that need to be addressed in further challenges.

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Publication Details

Journal
Communications Chemistry
Published
2025-04-12
DOI
https://doi.org/10.1038/s42004-025-01507-0
Citations
11
Primary Topic
RNA modifications and cancer
Type
article
Field-Weighted Citation Impact
8.87

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article

The RMaP challenge of predicting RNA modifications by nanopore sequencing

Mark Helm, Susanne Gerber, Vincent Dietrich, Anne Busch et al.
11 citations
Communications Chemistry
RNA modifications and cancer
8.87
article

The RMaP challenge of predicting RNA modifications by nanopore sequencing

Mark Helm, Susanne Gerber, Vincent Dietrich, Anne Busch, Winfried Göettsch, Stefan Mündnich, Andreas Hildebrandt, Manja Marz, Jannes Spangenberg, Anna Wierczeiko, Salvatore Di Giorgio, Leszek P. Pryszcz, Eva Maria Novoa, Irem Tellioglu, Ranjan J. Perera, Yuk Kei Wan, Sonia Cruciani, Stefan Pastore, Nicolò Alagna, Jonathan Göke, Christoph Dieterich, Kandarp Joshi, Chi-Lam Poon, Paola Arrubarrena
article en
11 citations

Abstract

The field of epitranscriptomics is undergoing a technology-driven revolution. During past decades, RNA modifications like N6-methyladenosine (m<sup>6</sup>A), pseudouridine (ψ), and 5-methylcytosine (m<sup>5</sup>C) became acknowledged for playing critical roles in cellular processes. Direct RNA sequencing by Oxford Nanopore Technologies (ONT) enabled the detection of modifications in native RNA, by detecting noncanonical RNA nucleosides properties in raw data. Consequently, the field's cutting edge has a heavy component in computer science, opening new avenues of cooperation across the community, as exchanging data is as impactful as exchanging samples. Therefore, we seize the occasion to bring scientists together within the RNA Modification and Processing (RMaP) challenge to advance solutions for RNA modification detection and discuss ideas, problems and approaches. We show several computational methods to detect the most researched mRNA modifications (m<sup>6</sup>A, ψ, and m<sup>5</sup>C). Results demonstrate that a low prediction error and a high prediction accuracy can be achieved on these modifications across different approaches and algorithms. The RMaP challenge marks a substantial step towards improving algorithms' comparability, reliability, and consistency in RNA modification prediction. It points out the deficits in this young field that need to be addressed in further challenges.

Communications ChemistryVol. 8(1)
Agency for Science, Technology and Research (SG), Institució Catalana de Recerca i Estudis Avançats (ES), Turing Institute (GB), Memorial Sloan Kettering Cancer Center (US), Johns Hopkins University (US), National University of Singapore (SG), Universitat Pompeu Fabra (ES), German Cancer Research Center (DE), Johannes Gutenberg University Mainz (DE), Cornell University (US), Heidelberg University (DE), University Hospital Heidelberg (DE), University Medical Center of the Johannes Gutenberg University Mainz (DE), Johns Hopkins All Children's Hospital (US), Quantitative BioSciences (US), Jena Bioscience (Germany) (DE), Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) (DE), The Alan Turing Institute (GB), Centre for Genomic Regulation (ES), Sidney Kimmel Comprehensive Cancer Center (US), Weill Cornell Medicine (US), Imperial College London (GB), Genome Institute of Singapore (SG), Friedrich Schiller University Jena (DE)
Deutsche Forschungsgemeinschaft, Johannes Gutenberg-Universität Mainz
Partnerships for the goals
Openalex Percentile: Top 2%
RNA modifications and cancer
8.87
DOIOpen Access PDFOpenAlex
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