J Integr Plant Biol. ›› 2019, Vol. 61 ›› Issue (12): 1224-1242.DOI: 10.1111/jipb.12778

Special Issue: CRISPR

• Functional Omics and Systems Biology • Previous Articles     Next Articles

Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome

Yu Yang1†, Kai Tang1,2†, Tatsiana U Datsenka2†, Wenshan Liu2,3, Suhui Lv1, Zhaobo Lang1, Xingang Wang2, Jinghui Gao2,4, Wei Wang5,6, Wenfeng Nie1, Zhaoqing Chu5,6, Heng Zhang1, Avtar K Handa2, Jian-Kang Zhu2,7 and Huiming Zhang7*   

  1. 1. Shanghai Center for Plant Stress Biology, the Chinese Academy of Sciences, Shanghai 201602, China
    2. Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA
    3. State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
    4. College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
    5. Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
    6. Shanghai Chenshan Plant Science Research Center, the Chinese Academy of Sciences, Shanghai 201602, China
    7. Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai 200032, China

    These authors contributed equally to this work.
    *Correspondence:
    Email: Huiming Zhang (hmzhang@sibs.ac.cn)
  • Received:2019-01-02 Accepted:2019-01-14 Online:2019-01-16 Published:2019-12-01

Abstract: DNA methylation confers epigenetic regulation on gene expression and thereby on various biological processes. Tomato has emerged as an excellent system to study the function of DNA methylation in plant development. To date, regulation and function of DNA methylation maintenance remains unclear in tomato plants. Here, we report the critical function of tomato (Solanum lycopersicum) Methyltransferase 1 (SlMET1) in plant development and DNA methylome and transcriptome regulation. Using CRISPR‐Cas9 gene editing, we generated slmet1 mutants and observed severe developmental defects with a frame‐shift mutation, including small and curly leaves, defective inflorescence, and parthenocarpy. In leaf tissues, mutations in SlMET1 caused CG hypomethylation and CHH hypermethylation on a whole‐genome scale, leading to a disturbed transcriptome including ectopic expression of many RIN target genes such as ACC2 in leaf tissues, which are normally expressed in fruits. Neither the CG hypomethylation nor CHH hypermethylation in the slmet1 mutants is related to tissue culture. Meanwhile, tissue culture induces non‐CG hypomethylation, which occurs more frequently at gene regions than at TE regions. Our results depict SlMET1‐ and tissue culture‐dependent tomato DNA methylomes, and that SlMET1 is required for maintaining a normal transcriptome and normal development of tomato.

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