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Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [WGBS]

ABSTRACT: Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [WGBS]

PROVIDER: PRJNA758397 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15657162_1.fastq.gz	Fastqsanger.gz
	SRR15657162_2.fastq.gz	Fastqsanger.gz
	SRR15657163_1.fastq.gz	Fastqsanger.gz
	SRR15657163_2.fastq.gz	Fastqsanger.gz
	SRR15657164_1.fastq.gz	Fastqsanger.gz

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Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish

Project description:Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish

| PRJNA758396 | ENA

Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [WGBS]

Project description:Here, we describe environmental Cu2+ in promoting zebrafish (Danio rerio) developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system, even the Cu2+ concentration is at 10 μg/L, the National Quality Standards of fishery water (GB11607-89); 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci-specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS, retina, and digestive system development during F1 embryogenesis; 3. Loci-specific hypoDMRs in the pmpcb promoter and loci-specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance, respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding, suggesting that environmental Cu2+ might pose a dramatic and long-lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis.

2022-08-27 | GSE182944 | GEO

Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA-Seq]

Project description:Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA-Seq]

| PRJNA758398 | ENA

Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA-Seq]

2022-08-27 | GSE182945 | GEO

Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish

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

2022-08-27 | GSE182946 | GEO

Comparison of Corynebacterium glutamicum cultivated under copper starvation with copper sufficiency

Project description:To identify genes which are differentially expressed in Corynebacterium glutamicum in the absence of copper, we performed DNA microarray analyses of cells cultivated under copper starvation conditions compared to copper sufficiency.

2018-08-28 | GSE117530 | GEO

Copper-induced stress mechanisms in Erwinia amylovora: a comparative phenotypic and transcriptomic study using copper-sensitive and -tolerant strains

Project description:Erwinia amylovora causes fire blight. Copper is widely used for fire blight management but there is limited information on the pathogen’s copper homeostasis mechanisms. Upon identifyingE. amylovora strains with unusually high (EaR2, Ea17) and intermediate (Ea19) copper sensitivity, we characterized them phenotypically to find potential correlations with other traits.The highly copper-sensitive strains EaR2 and Ea17 grew slower, showed increased sensitivity to paraquat and cadmium, and developed a characteristic copper-dependent overproduction of amylovoran and levan, with patterns not observed in strain, Ea273, with regular copper tolerance. Copper sensitivity was also associated with higher copper-shock death rates after copper pre-exposure during growth. RNA-Seq analysis revealed similar responses to copper-shock in EaR2 and Ea273 but very different transcriptomic responses during copper adaptation(prolonged growth with copper). EaR2 responded to copper adaptation with earlier activation ofstress responses, exopolysaccharide biosynthesis pathways, and protein quality control systems, while reducing the expression of genes linked to iron uptake. Ea273 mostly displayed an activation of copper homeostasis-related genes, with a characteristic downregulation of histidine catabolism.

2025-02-28 | GSE288253 | GEO

Copper-regulated genes of Bradyrhizobium japonicum

Project description:Copper-limiting growth conditions were thought to cause an induction of genes possibly involved in copper uptake and sorting. This rationale in mind, we performed microarray analyses on B. japonicum cells grown in three variations of the BVM minimal medium. Variant 1 contained 2 μM CuSO4 (copper excess). Variant 2 was prepared in HCl-treated glassware without any copper added (copper starvation). The residual copper concentration in this copper-starvation medium was analyzed by GF-AAS and determined to be 5 nM. Variant 3 (extreme copper limitation) was prepared like variant 2 but with the addition of 10 μM BCS and 1 mM ascorbic acid where BCS chelates Cu(I) selectively, and ascorbic acid reduces any Cu(II) to Cu(I). Changes in the transcription profiles were recorded by the pairwise comparison of cells grown in variant 2 vs. 1, and variant 3 vs. 2. Only a small set of genes were differentially up- or down-regulated when copper-starved cells were compared with cells grown in copper excess. Most notably, five genes located adjacent to each other on the B. japonicum genome displayed an increased expression: bll4882 to bll4878. The five genes were named pcuA, pcuB, pcuC, pcuD, and pcuE (mnemonic of proteins for Cu trafficking). The genes with decreased expression are either of unknown function or – not surprisingly – play a role in copper resistance. Extreme copper limitation (variant 3 vs. 2) did not further enhance the expression of the five pcu genes. Instead, another cluster of adjacent genes was strongly up-regulated: bll0889 to bll0883, which code for unidentified transport functions. Incidentally, the list also includes the copper chaperone ScoI. Taken together, copper-limiting growth conditions have led to the de-repression of genes potentially involved in copper acquisition.

2012-10-01 | GSE40437 | GEO

The Arabidopsis copper transport protein COPT2 and the responses under copper and iron deficiency.

Project description:Copper and iron are essential micronutrients for most living organisms because they participate as cofactors in biological processes including respiration, photosynthesis and oxidative stress protection. In many eukaryotic organisms, including yeast and mammals, copper and iron homeostases are highly interconnected; however such interdependence is not well established in higher plants. Here we propose that COPT2, a high-affinity copper transport protein, functions under copper and iron deficiencies in Arabidopsis thaliana. COPT2 is a plasma membrane protein that functions in copper acquisition and distribution. Characterization of the COPT2 expression pattern indicates a synergic response to copper and iron limitation in roots. We have characterized a knockout of COPT2, copt2-1, that leads to increased resistance to simultaneous copper and iron deficiencies, measured as reduced leaf chlorosis and improved maintenance of the photosynthetic apparatus. We propose that COPT2 expression could play a dual role under Fe deficiency. First, COPT2 participates in the attenuation of copper deficiency responses driven by iron limitation maybe aimed to minimize further iron consume. On the other hand, global expression analyses of copt2-1 mutants versus wild type Arabidopsis plants indicate that low phosphate responses are increased in copt2-1 plants. In this sense, COPT2 function under Fe deficiency counteracts low phosphate responses. These results open up new biotechnological approaches to fight iron deficiency in crops.

2013-06-05 | GSE42642 | GEO

Large Copper

Project description:ORG.one project - Large Copper

| PRJEB75817 | ENA