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  • Review Article
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Epitranscriptome sequencing technologies: decoding RNA modifications

Nature Methods volume 14, pages 23–31 (2017)Cite this article

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An Erratum to this article was published on 28 February 2017

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Abstract

In recent years, major breakthroughs in RNA-modification-mediated regulation of gene expression have been made, leading to the emerging field of epitranscriptomics.Our understanding of the distribution, regulation and function of these dynamic RNA modifications is based on sequencing technologies. In this Review, we focus on the major mRNA modifications in the transcriptome of eukaryotic cells: N6-methyladenosine, N6, 2′-O-dimethyladenosine, 5-methylcytidine, 5-hydroxylmethylcytidine, inosine, pseudouridine and N1-methyladenosine. We discuss the sequencing technologies used to profile these epitranscriptomic marks, including scale, resolution, quantitative feature, pre-enrichment capability and the corresponding bioinformatics tools. We also discuss the challenges of epitranscriptome profiling and highlight the prospect of future detection tools. We aim to guide the choice of different detection methods and inspire new ideas in RNA biology.

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Figure 1: Chemical modifications in mRNA.
Figure 2: Transcriptome-wide sequencing methods for m6A.
Figure 3: Detecting m5C in the transcriptome.
Figure 4: ICE-seq.
Figure 5: Transcriptome-wide profiling of Ψ in the eukaryotic cells.
Figure 6: Mapping the m1A methylome.

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Change history

  • 10 February 2017

    In the version of this article initially published, author affiliation numbers were incorrect. Xiaoyu Li originally had affiliation 1; this has been changed to affiliations 1 and 2. Xushen Xiong originally had affiliations 1 and 2; these have been changed to affiliations 1–3. Chengqi Yi originally had affiliations 1 and 3; these have been changed to affiliations 2 and 4. The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We thank all members of the Yi laboratory for their insights and discussions. This work was supported by the National Basic Research Foundation of China (grant nos. MOST2016YFC0900300 and 2014CB964900) and the National Natural Science Foundation of China (grant no. 21522201).

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Authors and Affiliations

  1. State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China

    Xiaoyu Li & Xushen Xiong

  2. Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China

    Xiaoyu Li, Xushen Xiong & Chengqi Yi

  3. Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China

    Xushen Xiong

  4. Synthetic and Functional Biomolecules Center and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China

    Chengqi Yi

Authors
  1. Xiaoyu Li
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  2. Xushen Xiong
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  3. Chengqi Yi
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Corresponding author

Correspondence to Chengqi Yi.

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The authors declare no competing financial interests.

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Li, X., Xiong, X. & Yi, C. Epitranscriptome sequencing technologies: decoding RNA modifications. Nat Methods 14, 23–31 (2017). https://doi.org/10.1038/nmeth.4110

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  • DOI: https://doi.org/10.1038/nmeth.4110

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