Science China Life Sciences

, Volume 61, Issue 11, pp 1293–1300 | Cite as

Manipulating mRNA splicing by base editing in plants

  • Chenxiao Xue
  • Huawei Zhang
  • Qiupeng Lin
  • Rong Fan
  • Caixia GaoEmail author
Cover Article


Precursor-mRNAs (pre-mRNA) can be processed into one or more mature mRNA isoforms through constitutive or alternative splicing pathways. Constitutive splicing of pre-mRNA plays critical roles in gene expressional regulation, such as intron-mediated enhancement (IME), whereas alternative splicing (AS) dramatically increases the protein diversity and gene functional regulation. However, the unavailability of mutants for individual spliced isoforms in plants has been a major limitation in studying the function of mRNA splicing. Here, we describe an efficient tool for manipulating the splicing of plant genes. Using a Cas9-directed base editor, we converted the 5′ splice sites in four Arabidopsis genes from the activated GT form to the inactive AT form. Silencing the AS of HAB1.1 (encoding a type 2C phosphatase) validated its function in abscisic acid signaling, while perturbing the AS of RS31A revealed its functional involvement in plant response to genotoxic treatment for the first time. Lastly, altering the constitutive splicing of Act2 via base editing facilitated the analysis of IME. This strategy provides an efficient tool for investigating the function and regulation of gene splicing in plants and other eukaryotes.


base editing splicing intron retention alternative 5′ splicing site 


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This work was supported by grants from the National Key Research and Development Program of China (2016YFD0101804), the National Natural Science Foundation of China (31788103 and 31420103912), as well as the Chinese Academy of Sciences (QYZDY-SSW-SMC030 and GJHZ1602).

Supplementary material

11427_2018_9392_MOESM1_ESM.docx (869 kb)


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Copyright information

© Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Chenxiao Xue
    • 1
    • 2
  • Huawei Zhang
    • 1
  • Qiupeng Lin
    • 1
    • 2
  • Rong Fan
    • 1
    • 2
    • 3
  • Caixia Gao
    • 1
    • 2
    Email author
  1. 1.State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
  2. 2.University of Chinese Academy of SciencesBeijingChina
  3. 3.Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina

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