title: Requirement of CHROMOMETHYLASE3 for somatic inheritance of the spontaneous tomato epimutation Colourless non-ripening.
abstract: Naturally-occurring epimutants are rare and have mainly been described in plants. However how these mutants maintain their epigenetic marks and how they are inherited remain unknown. Here we report that CHROMOMETHYLASE3 (SlCMT3) and other methyltransferases are required for maintenance of a spontaneous epimutation and its cognate Colourless non-ripening (Cnr) phenotype in tomato. We screened a series of DNA methylation-related genes that could rescue the hypermethylated Cnr mutant. Silencing of the developmentally-regulated SlCMT3 gene results in increased expression of LeSPL-CNR, the gene encodes the SBP-box transcription factor residing at the Cnr locus and triggers Cnr fruits to ripen normally. Expression of other key ripening-genes was also up-regulated. Targeted and whole-genome bisulfite sequencing showed that the induced ripening of Cnr fruits is associated with reduction of methylation at CHG sites in a 286-bp region of the LeSPL-CNR promoter, and a decrease of DNA methylation in differentially-methylated regions associated with the LeMADS-RIN binding sites. Our results indicate that there is likely a concerted effect of different methyltransferases at the Cnr locus and the plant-specific SlCMT3 is essential for sustaining Cnr epi-allele. Maintenance of DNA methylation dynamics is critical for the somatic stability of Cnr epimutation and for the inheritance of tomato non-ripening phenotype.
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Chen
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Junhua
authors.initials: J
authors.lastname: Kong
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Qin
authors.affiliation: State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong.
authors.forename: Sheng
authors.initials: S
authors.lastname: Yu
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Jinjuan
authors.initials: J
authors.lastname: Tan
authors.affiliation: State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong.
authors.forename: Yun-ru
authors.initials: YR
authors.lastname: Chen
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Chaoqun
authors.initials: C
authors.lastname: Wu
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
authors.affiliation: School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
authors.forename: Yan
authors.initials: Y
authors.lastname: Shi
authors.affiliation: School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
authors.forename: Chunyang
authors.initials: C
authors.lastname: Li
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Li
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Pengcheng
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Tongfei
authors.initials: T
authors.lastname: Lai
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Yu
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Xian
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Nongnong
authors.initials: N
authors.lastname: Shi
authors.affiliation: Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
authors.forename: Huizhong
authors.initials: H
authors.lastname: Wang
authors.affiliation: School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
authors.forename: Toba
authors.initials: T
authors.lastname: Osman
authors.affiliation: MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Yule
authors.initials: Y
authors.lastname: Liu
authors.affiliation: School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Manning
authors.affiliation: School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
authors.forename: Stephen
authors.initials: S
authors.lastname: Jackson
authors.affiliation: UMR Fruit Biology and Pathology, Bordeaux University, INRA, Villenave d'Ornon 33883, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Rolin
authors.affiliation: State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong.
authors.forename: Silin
authors.initials: S
authors.lastname: Zhong
authors.affiliation: Plant and Crop Science Division, School of Biosciences, University of Nottingham, Loughborough, Leics LE12 5RD, UK.
authors.forename: Graham B
authors.initials: GB
authors.lastname: Seymour
authors.affiliation: UMR Fruit Biology and Pathology, Bordeaux University, INRA, Villenave d'Ornon 33883, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Gallusci
authors.affiliation: 1] Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China [2] School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
authors.forename: Yiguo
authors.initials: Y
authors.lastname: Hong
mesh_terms: D000483:Alleles; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005030:Ethylenes / Q000096:biosynthesis; D005638:Fruit; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D055106:Genome-Wide Association Study; D018551:Solanum lycopersicum / Q000235:genetics* / Q000378:metabolism*; D009154:Mutation; D010641:Phenotype; D011401:Promoter Regions, Genetic; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D005030:Ethylenes; D014157:Transcription Factors; D004248:DNA (Cytosine-5-)-Methyltransferases; C112810:chromomethylase