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Epitranscriptomic technologies and analyses

  • Review
  • Special Topic: Noncoding RNA: from dark matter to bright star
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Abstract

RNA can interact with RNA-binding proteins (RBPs), mRNA, or other non-coding RNAs (ncRNAs) to form complex regulatory networks. High-throughput CLIP-seq, degradome-seq, and RNA-RNA interactome sequencing methods represent powerful approaches to identify biologically relevant ncRNA-target and protein-ncRNA interactions. However, assigning ncRNAs to their regulatory target genes or interacting RNA-binding proteins (RBPs) remains technically challenging. Chemical modifications to mRNA also play important roles in regulating gene expression. Investigation of the functional roles of these modifications relies highly on the detection methods used. RNA structure is also critical at nearly every step of the RNA life cycle. In this review, we summarize recent advances and limitations in CLIP technologies and discuss the computational challenges of and bioinformatics tools used for decoding the functions and regulatory networks of ncRNAs. We also summarize methods used to detect RNA modifications and to probe RNA structure.

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Authors and Affiliations

  1. State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China

    Xiaoyu Li, Jinying Peng & Chengqi Yi

  2. MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China

    Qiao-Xia Liang, Jin-Ran Lin, Jian-Hua Yang & Ke-Ren Zhou

  3. The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, 519000, China

    Jian-Hua Yang

  4. Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China

    Chengqi Yi

  5. Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China

    Yang Yu

  6. MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China

    Qiangfeng Cliff Zhang

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  1. Xiaoyu Li
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  4. Jinying Peng
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  7. Yang Yu
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Prof. Chengqi Yi’s team wrote RNA modifications, Prof. Jian-Hua Yang’s team wrote bioinformatics methods, Prof. Qiangfeng Zhang’s team wrote RNA structures, and Prof. Yang Yu’s team wrote biological methods for RNA-protein interaction.

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Correspondence to Jian-Hua Yang, Chengqi Yi, Yang Yu or Qiangfeng Cliff Zhang.

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The authors contributed equally to this work and are arranged in alphabetic order of surnames.

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Li, X., Liang, QX., Lin, JR. et al. Epitranscriptomic technologies and analyses. Sci. China Life Sci. 63, 501–515 (2020). https://doi.org/10.1007/s11427-019-1658-x

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