Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum

Cao, Deliang; Zheng, Jie; Gao, Chao; Mei, Xiaohong; Fu, Daqi; Zhu, Hongliang; Luo, Yunbo; Zhu, Beiwei

doi:10.1016/j.gene.2014.08.034

Cited by 53 publications

(74 citation statements)

References 35 publications

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“…6). These results are consistent with the location of DNA methylation in plant cell nuclei and suggest their possible function in tomato (Cao et al 2014). (1-32)K9me2 peptide.…”

Section: Subcellular Localization Of Tomato Cmtssupporting

confidence: 86%

“…The gene structure analysis was performed mostly using the genomic information present at SGN (http://solgenomics.net/). The existing nomenclature was followed for naming the tomato DMTases (Cao et al 2014, Chen et al 2015. The remaining DMTases in other Solanaceae species were renamed based on the relative sequence similarity to their tomato homologs (Table 1; Supplemental Table S1 in supplemental file S1).…”

Section: Gene Structure and Phylogenetic And Syntenic Analysis Of Solmentioning

confidence: 99%

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Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae

Kumar

Chauhan

Khurana

2016

Funct Integr Genomics

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DNA methyltransferase (DMTase) enzymes contribute to plant development and stress responses by de novo establishment and subsequent maintenance of DNA methylation during replication. However, the molecular mechanism underlying this activity remains obscure, especially in crop species. Using DMTase homolog complement in six Solanaceae species, we demonstrated here that their number remained conserved in Solanum lineage, whereas it was expanded in both pepper and Nicotiana benthamiana. Non-synonymous vs synonymous (Ka/Ks) substitution ratio revealed that most of the Solanaceous DMTase homologs undergo purifying selection. The genomic sequences of tomato DMT homologs in its wild relative, Solanum pennellii, remained highly conserved in their exons and methyltransferase domains. Structure analysis further revealed highly similar folding of DMTase homologs and conservation in the residues participating in protein-protein interaction in Solanum lineage, whereas a considerable diversification was observed of pepper homologs. Transcript profiling of DMTases highlighted both similar and distinct expression patterns of tomato homologs in other species during fruit development and stress responses. Overall, our analysis provides a strong basis for in-depth exploration of both conserved as well as distinct functions of tomato DMTase homologs in other economically important Solanaceae species.

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“…6). These results are consistent with the location of DNA methylation in plant cell nuclei and suggest their possible function in tomato (Cao et al 2014). (1-32)K9me2 peptide.…”

Section: Subcellular Localization Of Tomato Cmtssupporting

confidence: 86%

Section: Gene Structure and Phylogenetic And Syntenic Analysis Of Solmentioning

confidence: 99%

Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae

Kumar

Chauhan

Khurana

2016

Funct Integr Genomics

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“…During tomato fruit ripening, DNA demethylation occurs in numerous genomic regions (27). In tomato, there are four annotated 5-mC DNA glycosylase/DNA demethylase genes; one of them, SlDML2, is highly induced during fruit ripening (29,30). A recent study using RNAi lines of the demethylases suggested that SlDMLs-mediated active DNA demethylation is important for fruit ripening (29).…”

Section: Resultsmentioning

confidence: 99%

“…Tomato contains four putative DNA demethylases (SlDML1 to -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 (AtROS1) (29,30). A previous study used RNAi against the conserved HhH-GPD domain to investigate the function of SlDMLs in tomato (29).…”

mentioning

confidence: 99%

Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit

Lang

YiHai

Tang

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

394

409

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DNA methylation is a conserved epigenetic mark important for genome integrity, development, and environmental responses in plants and mammals. Active DNA demethylation in plants is initiated by a family of 5-mC DNA glycosylases/lyases (i.e., DNA demethylases). Recent reports suggested a role of active DNA demethylation in fruit ripening in tomato. In this study, we generated loss-of-function mutant alleles of a tomato gene, SlDML2, which is a close homolog of the Arabidopsis DNA demethylase gene ROS1. In the fruits of the tomato mutants, increased DNA methylation was found in thousands of genes. These genes included not only hundreds of ripening-induced genes but also many ripening-repressed genes. Our results show that SlDML2 is critical for tomato fruit ripening and suggest that active DNA demethylation is required for both the activation of ripeninginduced genes and the inhibition of ripening-repressed genes.DNA demethylase | 5-mC DNA glycosylase | DNA methylation | epigenetic regulation | gene silencing D NA methylation is a conserved epigenetic modification that is generally associated with inactive transcription in plants and mammals. As such, DNA methylation plays important roles in many biological processes, such as genome stability, gene imprinting, development, and response to the environment (1-3). In contrast to mammals, in which DNA methylation predominantly occurs at cytosines in the symmetric CG sequence context, plants commonly have methylation in the asymmetrical CHH sequence context (H = A, C, or T), as well as in the symmetrical CG and CHG contexts (1, 2). In plants, cytosines in all sequence contexts can be de novo methylated through the well-known RNA-directed DNA methylation pathway (RdDM), in which 24-nt siRNAs guide the DNA methyltransferase domains rearranged methyltransferase 2 (DRM2) to methylate target loci (4). DNA methylation can be maintained during replication; mCG and mCHG are maintained by the DNA methyltransferases DNA methyltransferase 1 (MET1) and chromomethylase 3 (CMT3), respectively, whereas mCHH is maintained by CMT2 and RdDM (4, 5).Cytosine methylation levels are dynamically regulated by DNA methylation and demethylation reactions (3, 6). DNA methylation can be lost either because of failure in maintaining methylation after replication (i.e., passive DNA demethylation) or because of active removal by enzymes (i.e., active DNA demethylation). Previous studies have identified and characterized several enzymes important for active DNA demethylation in Arabidopsis (7-11). The ROS1 family of bifunctional 5-methylcytosine DNA glycosylases/lyases, often referred to as DNA demethylases, initiate active DNA demethylation by removing the methylcytosine base from the DNA backbone, resulting in a single nucleotide gap that can be filled with an unmethylated cytosine through a base excision repair pathway (7,8,12,13). Several enzymes acting downstream of ROS1, such as the 3′ DNA phosphatase ZDP, AP endonuclease-like protein APE1L, and DNA ligase I (AtLIG1), have also been identified ...

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“…Genomic DNA cytosine methylation from tomato pericarps was decreased prior to ripening initiation (Cao et al, 2014). The expression level of Solyc12g100330.1 was 17-fold elevated in 1-MCP treated tomato fruits (Table 6).…”

Section: Analysis Of Genes Involved In Cell Wall Degradationmentioning

confidence: 97%

Transcriptomic Analysis on the Regulation of Tomato Ripening by the Ethylene Inhibitor 1-methylcyclopropene

Bobokalonov¹,

Liu²,

Shahrin³

et al. 2018

JPS

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Tomato is a climacteric fruit whose ripening is regulated by the plant hormone ethylene. 1-methylcyclopropene (1-MCP) is a competitive ethylene inhibitor that can delay the fruit ripening process. To understand the molecular mechanism of how 1-MCP inhibits tomato fruit ripening, transcriptomics (RNA-Seq) was used to identify genes that were differentially expressed in 1-MCP-treated (Day 1) tomato fruits. Of the 35340 genes in the tomato genome, about 50% were expressed with 1-MCP treatment. There were 5683 genes identified as significantly differentially expressed. Quantitative reverse transcription PCR (qRT-PCR) assays were used to validate the RNA-Seq data. Our results showed that 1-MCP treatment resulted in the down-regulation of fruit ripening-related genes, including genes involved in ethylene synthesis, signal transduction and carotenoid biosynthesis. Our results provide insight at the whole genome level regarding gene regulation by 1-MCP during fruit ripening. Understanding the molecular basis of 1-MCP inhibition on tomato ripening may help farmers and food processors to better use 1-MCP in agriculture and food industry.

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Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum

Cited by 53 publications

References 35 publications

Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae

Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae

Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit

Transcriptomic Analysis on the Regulation of Tomato Ripening by the Ethylene Inhibitor 1-methylcyclopropene

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