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Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE142714 | GEO | 2020/04/13

REPOSITORIES: GEO

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Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato [RNA-Seq]

Project description:Here, we found that the tomato jmjC domain-containing gene SlJMJ6 encodes a histone lysine demethylase that specifically demethylates H3K27 methylation. Overexpression of SlJMJ6 accelerated fruit ripening in tomato, which is associated with the up-regulated expression of a large number of ripening-related genes. Integrated analysis of RNA-seq and ChIP-seq data identified 55 genes that are targeted directly by SlJMJ6 and transcriptionally up-regulated with decreased H3K27m3 in SlJMJ6 overexpressing (SlJMJ6-OE) fruits. A large number of the SlJMJ6-regulated genes are involved in transcription regulation, ethylene biosynthesis, cell wall degradation, pigment biosynthesis, and hormone signaling. Fourteen ripening-related genes including RIN, ACS4, ACO1, PL, TBG4 were confirmed to be directly regulated by SlJMJ6 through removing H3K27me3. Taken together, these results indicated that SlJMJ6 is a ripening prompting H3K27me3 demethylase that activates the expression of the ripening-related genes by modulating H3K27me3, thereby facilitating fruit ripening in tomato. To our knowledge, this is the first report of the involvement of a histone lysine demethylase in the regulation of fruit ripening.

2020-04-13 | GSE142713 | GEO

Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato [ChIP-Seq]

2020-04-13 | GSE142712 | GEO

Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato

Project description:Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato

| PRJNA598111 | ENA

Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato [RNA-Seq]

Project description:Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato [RNA-Seq]

| PRJNA598113 | ENA

Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato [ChIP-Seq]

Project description:Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato [ChIP-Seq]

| PRJNA598114 | ENA

A DEMETER-like DNA demethylase governs tomato fruit ripening.

Project description:In plants, genomic DNA methylation which contributes to development and stress responses can be actively removed by DEMETER-like DNA demethylases (DMLs). Indeed, in Arabidopsis DMLs are important for maternal imprinting and endosperm demethylation, but only a few studies demonstrate the developmental roles of active DNA demethylation conclusively in this plant. Here, we show a direct cause and effect relationship between active DNA demethylation mainly mediated by the tomato DML, SlDML2, and fruit ripening- an important developmental process unique to plants. RNAi SlDML2 knockdown results in ripening inhibition via hypermethylation and repression of the expression of genes encoding ripening transcription factors and rate-limiting enzymes of key biochemical processes such as carotenoid synthesis. Our data demonstrate that active DNA demethylation is central to the control of ripening in tomato.

| S-EPMC4553810 | biostudies-literature

Proteome-wide identification of non-histone lysine methylation in tomato during fruit ripening.

Project description:IntroductionHistone and non-histone methylations are important post-translational modifications in plants. Histone methylation plays a crucial role in regulating chromatin structure and gene expression. However, the involvement of non-histone methylation in plant biological processes remains largely unknown.MethodsThe methylated substrates and methylation sites during tomato fruit ripening were identified by LC-MS/MS. Bioinformatics of lysine methylated proteins was conducted to analyze the possible role of methylated proteins. The effects of methylation modification on protein functions were preliminarily investigated by site-directed mutation simulation.ResultsA total of 241 lysine methylation (mono-, di- and trimethylation) sites in 176 proteins were identified with two conserved methylation motifs: xxxxxxExxx_K_xxxExxxxxx and xxxxxxExxx_K_xxxxxxxxxx. These methylated proteins were mainly related to fruit ripening and senescence, oxidation reduction process, signal transduction, stimulus and stress responses, and energy metabolism. Three representative proteins, thioredoxin (Trx), glutathione S-transferase T1 (GST T1), and NADH dehydrogenase (NOX), were selected to investigate the effect of methylation modifications on protein activity. Mimicking demethylation led to decreased Trx activity but increased GST T1 and NOX activities. In addition, RT-qPCR exhibited that the expression of many genes that encode proteins subjected to methylation was upregulated during fruit ripening.ConclusionOur study suggests that tomato fruit ripening undergo non-histone lysine methylation, which may participate in the regulation of fruit ripening. It is the first report of methyl proteome profiling of non-histone lysine in horticultural crops.

| S-EPMC9788949 | biostudies-literature

Histone demethylase SlJMJ4 promotes leaf senescence via removal of H3K27 methylation of senescence-related genes in tomato

Project description:SlJMJ4 is a positive regulator of leaf senescence in tomato and mediates ABA-induced leaf senescence by activating the transcription of many genes related to ABA synthesis and signaling, and transcription regulation via removal of their H3K27me3 levels.

2022-04-06 | GSE177487 | GEO

Histone demethylase SlJMJ7 Integrates DNA demethylation, ethylene signal and major ripening-related transcription factors in coordination of fruit ripening in tomato

Project description:Combinational analyses of genome-wide transcription, binding sites and histone H3K4 trimethylation profiles revealed that SlJMJ7 directly binds and represses the expression of a series of key ripening-associated factors, including ethylene biosynthesis genes ACS2/4/8 and ACO2, DNA demethylase DML2, as well as the ripening-related transcription factors RIN and NOR by removal the mark of H3K4-trimethylation. Moreover, SlJMJ7 directly and indirectly modulates the transcription of genes related to diverse physiological traits of fruit ripening.

2021-06-22 | GSE153080 | GEO

Histone demethylase SlJMJ7 integrates DNA demethylation, ethylene signal and major ripening-related transcription factors in coordination of fruit ripening in tomato.

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-07-10 | GSE148527 | GEO