Photodamage repair pathways contribute to the accurate maintenance of DNA methylome landscape upon UV exposure
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ABSTRACT:
PROVIDER: PRJNA548919 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9302980_1.fastq.gz | Fastqsanger.gz | |||
| SRR9302980_2.fastq.gz | Fastqsanger.gz | |||
| SRR9302990.fastq.gz | Fastqsanger.gz | |||
| SRR9303000_1.fastq.gz | Fastqsanger.gz | |||
| SRR9303000_2.fastq.gz | Fastqsanger.gz |
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Project description:UV irradiation is a major environmental effector of skin damage and aging. Elevated levels of glycosaminoglycans (GAGs), as measured by Hale’s stain, are seen following cutaneous photodamage. Preliminary data from our lab indicates that this is a complex response involving differential regulation of both GAGs and proteoglycans. Recently, different GAG species have been shown to have distinct effects on the recruitment and activation of immune cells and stimulation of cytokine production (Taylor and Gallo, FASEB, 2006; 20: 9-22). We speculate that the elevated GAGs and proteoglycans observed after ultraviolet B (UVB) irradiation are involved in the inflammatory and healing responses to photodamage.
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Project description:Exposure to UV-C irradiance effectively maintains fruit quality, however the mechanisms by which it ensures tomato postharvest quality remain unclear. We conducted a comprehensive analysis of the transcriptome, volatilome, DNA methylome, and RNA methylome of tomato fruit in order to construct a UV-C regulatory network. UV-C was found to induce the expression of hormones-related, flavonoid, and resistance genes, to delay senescence, and to promote the expression of sugar and acid metabolism genes, leading to the synthesis of soluble sugars and degradation of citric acid in a manner that maintains fruit taste characteristics. Volatilome results demonstrated that UV-C enhanced the accumulation of 3-methyl-2-butenal, β-damascenone, and 6-methyl-5-heptene-2-one by regulating genes associated with the metabolism of these volatile organic compounds. Additionally, UV-C contributed to the retention of accessible chromatin regions (ACRs), with genes associated with plant hormones showing variation in expression corresponding to chromatin accessibility. UV-C also inhibited the decrease in DNA methylation during ripening, with dynamic changes in DNA methylation and RNA methylation of genes related to hormones, flavonoids, texture, and resistance, ultimately delaying fruit senescence. This study is the first to comprehensively elucidate the regulatory role of UV-C on tomato postharvest ripening and as such provides valuable insights into epigenetic modifications which could represent important tools for future quality-based breeding programs.
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Project description:UV irradiation is a major environmental effector of skin damage and aging. Elevated levels of glycosaminoglycans (GAGs), as measured by Hale’s stain, are seen following cutaneous photodamage. Preliminary data from our lab indicates that this is a complex response involving differential regulation of both GAGs and proteoglycans. Recently, different GAG species have been shown to have distinct effects on the recruitment and activation of immune cells and stimulation of cytokine production (Taylor and Gallo, FASEB, 2006; 20: 9-22). We speculate that the elevated GAGs and proteoglycans observed after ultraviolet B (UVB) irradiation are involved in the inflammatory and healing responses to photodamage. Chondroitin sulfate synthases (CSSs) are not increased by UVB in mice or in cultured human fibroblasts. To determine whether genomic upregulation of CSSs is responsible for the post-UVB CS increase, we measured the dermal expression of CSS1 and CSS3 mRNA in C57Bl6 mice after 5 days of UV-B exposure. Irradiation caused no change in either CSS1 or CSS3 mRNA expression. We also studied CSS RNA expression in cultured human fibroblasts. We compared control cells to cells treated with 30 mJ/cm2 UVB, cells treated with 1 ng/mL IL-1α, and cells co-stimulated with UVB and IL-1α. In vivo, UV-B induces IL-1α production by keratinocytes and inflammatory cells, and this IL-1α interacts with fibroblasts. Co-stimulation with IL-1α + UVB induces TNF-α production by the fibroblasts, mirroring the in vivo interaction. CSS1 mRNA was suppressed 60% and CSS3 mRNA expression dropped 87% relative to sham at 24 hours post-treatment (p<0.001, Dunnet q’). Since CS is not upregulated by its synthases, we postulated an alternative mode of induction whereby one or more CS proteoglycans are transcriptionally increased and bind more CS in the dermis. We used the N-13 goat monoclonal anti-serglycin antibody to visualize changes in cutaneous serglycin content following acute UV-B exposure. Serglycin is one example of CS-binding dermal proteoglycans that is induced by UVB, and there are likely others. Diffuse upper-dermal serglycin staining, like upper-dermal CS, was induced continuously at 24, 48, and 72 hours after irradiation. Serglycin-expressing inflammatory cells are recruited to the dermis following irradiation, peaking at 48 hours post-exposure. A statistically significant 1.70 fold increase in serglycin mRNA was measured in cultured human fibroblasts 6 hours after co-stimulation with UVB and IL-1α. Realtime PCR also revealed a significant 2.04 fold upregulation at 24 hours after co-stimulation, and serglycin was increased 4.63 times 6 hours after Il-1α treatment alone.
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