Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [pre-experiment]
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ABSTRACT:
PROVIDER: PRJNA719810 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14144741_1.fastq.gz | Fastqsanger.gz | |||
| SRR14144741_2.fastq.gz | Fastqsanger.gz | |||
| SRR14144742_1.fastq.gz | Fastqsanger.gz | |||
| SRR14144742_2.fastq.gz | Fastqsanger.gz | |||
| SRR14144743_1.fastq.gz | Fastqsanger.gz |
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Project description:Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [green fruit]
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Project description:DNA methylation is a conserved epigenetic mark that influences diverse biological processes in many eukaryotes. Recently, DNA methylation was proposed to regulate fleshy fruit ripening. Fleshy fruits can be distinguished by their ripening process as climacteric fruits, such as tomatoes, or non-climacteric fruits, such as strawberries. Tomatoes undergo a global decrease in DNA methylation during ripening, due to increased expression of a DNA demethylase gene. The dynamics and biological relevance of DNA methylation during ripening of non-climacteric fruits, or other climacteric fruits, are unknown. Here, we generated and characterized single-base resolution maps of the DNA methylome in strawberry fruit, from immature to ripe stages. We observed an overall loss of DNA methylation during strawberry fruit ripening. Thus, ripening-induced DNA hypomethylation occurs not only in climacteric fruit, but also in non-climacteric fruit. However, we discovered that the mechanisms underlying DNA hypomethylation during ripening of tomato and strawberry are distinct. Unlike in tomatoes, DNA demethylase genes were not up-regulated during ripening of strawberries. Instead, genes involved in RNA-directed DNA methylation were down-regulated during strawberry ripening. Further, ripening-induced DNA hypomethylation was associated with decreased siRNA levels, consistent with reduced RdDM activity. Therefore, we propose that DNA hypomethylation during strawberry ripening is caused by diminished RdDM activity. Finally, hundreds of ripening-related genes displayed altered expression that was associated with, and thus potentially regulated by, DNA hypomethylation during ripening. Our findings provide new insight into the DNA methylation dynamics during the ripening of non-climateric fruit and reveal a novel function of RdDM in regulating an important process in plant development.
2018-11-13 | GSE113084 | GEO
Project description:Proteomics shotgun approach used to uncover proteins involved in peach fruit mesocarp ripening process.
2020-11-25 | MSV000086519 | MassIVE
Project description:Fruit ripening in Citrus is not well understood at the molecular level. Knowledge of the regulatory mechanism of citrus fruit ripening at the post-transcriptional level in particular is lacking. Here, we comparatively analyzed the miRNAs and their targeted genes in a spontaneous late-ripening mutant, ?Fengwan? sweet orange (MT) (Citrus sinensis L. Osbeck), and its wild-type counterpart ('Fengjie 72-1', WT). Using high-throughput sequencing of small RNAs and RNA degradome tags, we identified 107 known and 21 novel miRNAs, as well as 225 target genes. A total of 24 miRNAs (16 known miRNAs and 8 novel miRNAs) were shown to be differentially expressed between MT and WT. The expression pattern of several key miRNAs and their target genes during citrus fruit development and ripening stages was examined. Csi-miR156k, csi-miR159 and csi-miR166d suppressed specific transcription factors (GAMYBs, SPLs and ATHBs) that are supposed to be important regulators involved in citrus fruit development and ripening. In the present study, miRNA-mediated silencing of target genes was found under complicated and sensitive regulation in citrus fruit. The identification of miRNAs and their target genes provide new clues for future investigation of mechanisms that regulate citrus fruit ripening.
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Project description:Transcription factors (TFs) are important regulators of plant growth and development and responses to stresses. TFs themselves are also susceptible to multiple post-translational modifications (PTMs). Relatively, redox-mediated PTM of TFs in plants is not well elucidated. Here, we found that NON-RIPENING (NOR), a master TF regulating tomato fruit ripening, is a target of SlMsrE4 or SlMsrB2, the methionine sulfoxide reductase A and B in tomato, respectively. Methionine oxidation in NOR, i.e. sulfoxidation, or mimicking sulfoxidation by mutating Met138 to glutamine, leads to the decreased DNA-binding capacity and transcriptional regulatory activity in vitro. On the other hand, SlMsrE4 and SlMsrB2 can partially repair oxidized-NOR and restore its DNA-binding capacity. Genetic transformation of the nor mutant with NOR genomic DNA almost completely rescues the ripening phenotype. However, transformation of nor with NOR-M138Q, the mimicked methionine sulfoxidation, inhibits the restore of fruit ripening phenotype, and this is associated with the decreased DNA-binding and transcriptional activation of numerous ripening-related genes. Taken together, these findings uncover a novel mechanism by which Msr-mediated redox modification of NOR regulates the expression of ripening-related genes, thereby influencing tomato fruit ripening. To our knowledge, this is the first report that redox modification of TF regulates fruit ripening. nor is a NOR mutant, the phenotype is obstructed by maturity; NOR-12 is a rotational NOR in NOR mutant, the phenotype is a mature inhibition phenotype that basically restores nor mutant; Nor-18 is a rotation of NOR-M138Q in nor mutant, phenotype with the effect of restoring maturity, but the recovery efficiency is lower than the swing NOR.
2020-05-22 | GSE140853 | GEO
Project description:[original title] Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes A tomato MADS-box transcription factor, LeMADS-RIN, controls fruit ripening and mutation in this gene results in non-ripening phenotype of fruit. This mutation down-regulates certain ripening related ethylene responses, however, other ethylene responses are normal. A complete understanding of this mutation and its effect on fruit transcriptome during ripening is not clear. In this study, microarray analysis has been used to investigate the influence of rin mutation on fruit transcriptome at different stages of ripening. A total of 2,398 genes were found to be differentially expressed in wild type fruit pericarp, which on cluster analysis indicated a major shift in their expression profiles in rin mutant fruit. A total of 1,802 genes were found to be differentially expressed between wild type and rin mutant fruits and 17% of these genes encoded regulatory elements, suggesting that mutation in LeMADS-RIN results in disturbance in the regulatory transcriptional networks during ripening. Since LeMADS-RIN has been reported to bind to the CArG box of LeACS2 promoter, in-silico analysis of 51 putative promoter sequences of the genes, that showed ripening associated up-regulation in wild type but showed impairment in up-regulation in rin mutant fruit during ripening, were searched for presence of CArG box along with ethylene and auxin responsive elements. The study revealed that only 24 putative promoter sequences harbor LeMADS-RIN specific CArG box suggesting an alternative mode of regulation by LeMADS-RIN for CArG box deficient genes.
2012-02-29 | GSE20720 | GEO
Project description:[original title] Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes A tomato MADS-box transcription factor, LeMADS-RIN, controls fruit ripening and mutation in this gene results in non-ripening phenotype of fruit. This mutation down-regulates certain ripening related ethylene responses, however, other ethylene responses are normal. A complete understanding of this mutation and its effect on fruit transcriptome during ripening is not clear. In this study, microarray analysis has been used to investigate the influence of rin mutation on fruit transcriptome at different stages of ripening. A total of 2,398 genes were found to be differentially expressed in wild type fruit pericarp, which on cluster analysis indicated a major shift in their expression profiles in rin mutant fruit. A total of 1,802 genes were found to be differentially expressed between wild type and rin mutant fruits and 17% of these genes encoded regulatory elements, suggesting that mutation in LeMADS-RIN results in disturbance in the regulatory transcriptional networks during ripening. Since LeMADS-RIN has been reported to bind to the CArG box of LeACS2 promoter, in-silico analysis of 51 putative promoter sequences of the genes, that showed ripening associated up-regulation in wild type but showed impairment in up-regulation in rin mutant fruit during ripening, were searched for presence of CArG box along with ethylene and auxin responsive elements. The study revealed that only 24 putative promoter sequences harbor LeMADS-RIN specific CArG box suggesting an alternative mode of regulation by LeMADS-RIN for CArG box deficient genes. Three chronological stages of tomato (Solanum lycopersicon) fruit ripening were compared between wild type and rin mutant
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2008-08-01 | GSE11246 | GEO