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mRNA m6A detection

Nature Reviews Methods Primers volume 4, Article number: 87 (2024) Cite this article

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Abstract

N6-methyladenosine (m6A) is the most prevalent internal mRNA modification. Recent research has highlighted its role as a key regulator of gene expression, influencing cellular processes and determining cell fate. Advances in techniques for global mapping of m6A, the discovery of m6A demethylases that enhance its dynamic properties and the identification of reader proteins that interact with m6A have substantially propelled this field forward. This Primer outlines the available tools for detecting and mapping m6A, discusses the strengths and limitations of each method and offers guidance on selecting the most suitable approach. Identifying and detecting m6A lays the groundwork for functional studies that address important biological and medical questions.

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Fig. 1: Proteins involved in m6A methylation of mRNA.
Fig. 2: Basic antibody-dependent m6A mapping tools.
Fig. 3: Isoform-aware and low input antibody-based methods.
Fig. 4: Metabolic labelling methods for mapping m6A.
Fig. 5: Additional methods for m6A profiling.

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Acknowledgements

The authors thank G. Moshkovitz for drawing the figures. This work was supported by the infrastructure grant of the Israel Innovation Authority, Israel Ministry of Health and the National Headquarter ‘Digital Israel’. The authors also thank the Kahn Family Foundation for continuous support of their research. D.D. is supported by grants from the Israel Science Foundation (2494/18 and 2625/17) and the Human Frontier Science Program (CDA 00048/2018). G.R. is supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 743168) and the Flight Attendant Medical Research Institute (FAMRI). G.R. and D.D. are supported by the German–Israeli Project Cooperation (DIP) of the German Federal Ministry of Education and Research and by a grant from the Varda and Boaz Dotan Research Center in Hemato-Oncology, Tel Aviv University. G.R. holds the Djerassi Chair in Oncology at the Tel Aviv University.

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Authors and Affiliations

  1. Cancer Research Center, Wohl Institute of Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel

    Sharon Moshitch-Moshkovitz, Reut Ashwal-Fluss, Efrat Glick-Saar, Gideon Rechavi & Dan Dominissini

  2. Tel Aviv University, Tel Aviv, Israel

    Sharon Moshitch-Moshkovitz, Michal Sevilla-Sharon & Dan Dominissini

  3. ARC Innovation Center, Sheba Medical Center, Tel Hashomer, Israel

    Efrat Glick-Saar & Gideon Rechavi

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  1. Sharon Moshitch-Moshkovitz
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  2. Michal Sevilla-Sharon
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Contributions

Introduction (G.R., S.M.-M., M.S.-S., and D.D.); Experimentation (S.M.-M., E.G.-S. and M.S.-S.); Results (E.G.-S., R.A.-F. and S.M.-M.); Applications (S.M.-M. and G.R.); Reproducibility and data deposition (R.A.-F.); Limitations and optimizations (S.M.-M. and G.R.); Outlook (S.M.-M. and G.R.); overview of the Primer (S.M.-M., G.R. and D.D.).

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Correspondence to Sharon Moshitch-Moshkovitz.

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Nature Reviews Methods Primers thanks Arne Klungland, Guan-Zheng Luo and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Related links

European Nucleotide Archive: https://www.ebi.ac.uk/ena/browser/submit

FastQC: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Gene Expression Omnibus: https://www.ncbi.nlm.nih.gov/geo/

Picard MarkDuplicates: https://broadinstitute.github.io/picard/

Sequence Read Archive: https://www.ncbi.nlm.nih.gov/sra

Trim Galore: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

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Moshitch-Moshkovitz, S., Sevilla-Sharon, M., Ashwal-Fluss, R. et al. mRNA m6A detection. Nat Rev Methods Primers 4, 87 (2024). https://doi.org/10.1038/s43586-024-00365-9

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