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Epigenetic Regulation of Tomato Fruit Ripening

DNA methylation is a conserved epigenetic modification that is generally associated with inactive transcription in plants and mammals, and the enzymes and regulatory factors involved in DNA demethylation are regarded as anti-silencing factors.

In tomato, fruits undergo a dramatic loss in DNA methylation during ripening, and application of DNA methylation inhibitor can facilitate fruit ripening. These results suggest that DNA methylation may play an important role in tomato fruit ripening. However, it is still unclear how DNA demethylation is involved in regulation of tomato fruit ripening.


Prof. ZHU Jiankang and Prof. LANG Zhaobo at Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, collaborating with researchers at Purdue University, find that SlDML2-mediated DNA demethylation is required for both the activation of ripening-induced genes and the inhibition of ripening-repressed genes, and thus required for tomato fruit ripening.


The Arabidopsis ROS1 family of bifunctional 5-methylcytosine DNA glycosylases/lyases, often referred to as DNA demethylases, can initiate active DNA demethylation by removing the methylcytosine base from the DNA backbone. Tomato contains four putative DNA demethylases (SlDML1-4) according to sequence homology with the Arabidopsis DNA demethylases, and two of them, SlDML1 and SlDML2, are most closely related to the Arabidopsis ROS1.

In this study, the research group generate loss-of-function mutant alleles of a tomato gene, SlDML2, which is a close homolog of the Arabidopsis DNA demethylase gene ROS1. They characterize the DNA methylomes of the mutant fruits failing to ripen and discover that SlDML2 is required for the demethylation and activation of genes for fruit ripening, including those involved in fruit pigment and flavor synthesis, ethylene synthesis and signaling, as well as cell wall hydrolysis.


Out of expectation, they find that SlDML2-mediated DNA demethylation is also necessary for fruit ripening-induced repression of hundreds of genes involved in photosynthesis and cell wall synthesis and organization. This study has therefore revealed a broad and critical role of DNA methylation as an activation mark for the expression of many genes in a eukaryotic organism.

This study, entitled “Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit”, was published in Proceedings of the National Academy of Sciences of the United States of America (PNAS) on May 15, 2017.

This research is supported by the Chinese Academy of Sciences.


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Author Contact:
ZHU Jiankang, Senior Principal Investigator
Shanghai Center for Plant Stress Biology (PSC),
CAS Center of Excellence in Molecular Plant Sciences
Shanghai Institute of Plant Physiology and Ecology (SIPPE)
Chinese Academy of Science (CAS)
Phone: (86) 21-57078201 
Fax: (86) 21- 57078213


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