RNA methylomes reveal the m(6)A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening

doi:10.1186/s13059-019-1771-7

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	RNA methylomes reveal the m(6)A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening
	Zhou, Leilei 1; Tian, Shiping 1; Qin, Guozheng
刊名	GENOME BIOLOGY
	2019
卷号	20 期号:1
关键词	Fruit ripening DNA methylation mRNA m(6)A methylation m(6)A RNA methylome RNA demethylase SlALKBH2 DNA demethylase SlDML2 Colorless non-ripening Tomato
ISSN号	1474-760X
DOI	10.1186/s13059-019-1771-7
文献子类	Article
英文摘要	Background Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N-6-methyladenosine (m(6)A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m(6)A in this process and the interplay between 5mC and m(6)A remain uncharacterized. Results Here, we show that mRNA m(6)A methylation exhibits dynamic changes similar to DNA methylation during tomato fruit ripening. RNA methylome analysis reveals that m(6)A methylation is a prevalent modification in the mRNA of tomato fruit, and the m(6)A sites are enriched around the stop codons and within the 3 ' untranslated regions. In the fruit of the ripening-deficient epimutant Colorless non-ripening (Cnr) which harbors DNA hypermethylation, over 1100 transcripts display increased m(6)A levels, while only 134 transcripts show decreased m(6)A enrichment, suggesting a global increase in m(6)A. The m(6)A deposition is generally negatively correlated with transcript abundance. Further analysis demonstrates that the overall increase in m(6)A methylation in Cnr mutant fruit is associated with the decreased expression of RNA demethylase gene SlALKBH2, which is regulated by DNA methylation. Interestingly, SlALKBH2 has the ability to bind the transcript of SlDML2, a DNA demethylase gene required for tomato fruit ripening, and modulates its stability via m(6)A demethylation. Mutation of SlALKBH2 decreases the abundance of SlDML2 mRNA and delays fruit ripening. Conclusions Our study identifies a novel layer of gene regulation for key ripening genes and establishes an essential molecular link between DNA methylation and mRNA m(6)A methylation during fruit ripening.
学科主题	Biotechnology & Applied Microbiology ; Genetics & Heredity
出版地	LONDON
WOS关键词	M(6)A RNA ; NUCLEAR-RNA ; DOMAIN PROTEIN ; CELL FATE ; METHYLATION ; ARABIDOPSIS ; N-6-METHYLADENOSINE ; EXPRESSION ; TRANSCRIPTOME ; WRITERS
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
语种	英语
出版者	BMC
WOS记录号	WOS:000479033800001
资助机构	National Natural Science Foundation of China (NSFC)National Natural Science Foundation of China (NSFC) [31871855, 31530057] ; Youth Innovation Promotion Association CAS [2011074]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/19893]
专题	中科院北方资源植物重点实验室
作者单位	1.Chinese Acad Sci, Innovat Acad Seed Design, Inst Bot, Key Lab Plant Resources, 20 Nanxincun, Beijing 100093, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Zhou, Leilei,Tian, Shiping,Qin, Guozheng. RNA methylomes reveal the m(6)A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening[J]. GENOME BIOLOGY,2019,20(1).
APA	Zhou, Leilei,Tian, Shiping,&Qin, Guozheng.(2019).RNA methylomes reveal the m(6)A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening.GENOME BIOLOGY,20(1).
MLA	Zhou, Leilei,et al."RNA methylomes reveal the m(6)A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening".GENOME BIOLOGY 20.1(2019).