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ABSTRACT: Environmentally induced DNA methylation is inherited across generations in water fleas (Daphnia magna)

PROVIDER: PRJNA760269 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15711007_1.fastq.gz	Fastqsanger.gz
	SRR15711007_2.fastq.gz	Fastqsanger.gz
	SRR15711008_1.fastq.gz	Fastqsanger.gz
	SRR15711008_2.fastq.gz	Fastqsanger.gz
	SRR15711009_1.fastq.gz	Fastqsanger.gz

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Genome-wide DNA Methylation Patterns in Daphnia magna Reveal Targeting to 5’ Exons

Project description:Daphnia magna is a widely used model organism in ecological and evolutionary studies. DNA methylation in D. magna can influence development and adaptation to changing environments. Previous studies have demonstrated that D. magna is generally hypomethylated. In this study we confirmed these observations using whole genome bisulfite sequencing (WGBS). In line with previous studies we observe that DNA methylation is elevated in the first exons downstream of the transcription start sites (TSS). Moreover, these exons are hypermethylated compared to adjacent introns. In contrast to prior studies in Daphnia, we found no significant changes in DNA methylation with age. These observations extend our understanding of the epigenetic landscape in D. magna, and motivate further exploration of epigenetic regulation in this organism and its response to environmental factors.

2024-07-05 | GSE267859 | GEO

Paternal diet induces transgenerational epigenetic inheritance of DNA methylation signatures and phenotypes in sheep model

Project description:We examined whether paternal diet from weaning to puberty induces sperm DNA methylation changes that can be transmitted to subsequent generations. Over 100 methylated cytosines environmentally altered in the F0 generation were inherited by the F1 and F2 generations. Furthermore, the F0 paternal diet was associated with growth and male fertility phenotypes in these generations. Differentially methylated genes also showed correlations with gene expression.

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Project description:Daphnia magna metagenomics across generations

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Using the Daphnia magna Transcriptome to Distinguish Water Source: Wetland and Stormwater Case Studies

Project description:Investigation of mRNA expression (using HiSeq 2500) in response to treatment of Daphnia magna to pyriproxyfen, wetland water, or stormwater samples.

2022-07-26 | GSE208591 | GEO

Transgenerational inheritance of DNA hypomethylation in Daphnia magna in response to salinity stress.

Project description:Epigenetic mechanisms have been found to play important roles in environmental stress response and regulation. These can, theoretically, be transmitted to future unexposed generations, yet few studies have shown persisting stress-induced transgenerational effects, particularly in invertebrates. Here, we focus on the aquatic microcrustacean Daphnia, a parthenogenetic model species, and its response to salinity stress. Salinity is a serious threat to freshwater ecosystems and a relevant form of environmental perturbation affecting freshwater ecosystems. We exposed one generation of D. magna to high levels of salinity (F0) and found that the exposure provoked specific methylation patterns that were transferred to the three consequent non-exposed generations (F1, F2 and F3). This was the case for the hypomethylation of six protein-coding genes with important roles in the organisms’ response to environmental change: DNA damage repair, cytoskeleton organization and protein synthesis. This suggests that epigenetic changes in Daphnia are particularly targeted to genes involved in coping with general cellular stress responses. Our results highlight that epigenetic marks are affected by environmental stressors and can be transferred to subsequent unexposed generations. Epigenetic marks could therefore prove to be useful indicators of past or historic pollution in this parthenogenetic model system. Furthermore, no life history costs seem to be associated with the maintenance of hypomethylation of across unexposed generations in Daphnia following a single stress exposure.

2018-08-20 | GSE107340 | GEO

Daphnia magna exposed to narcotics and polar narcotics

Project description:This SuperSeries is composed of the following subset Series: GSE29854: Daphnia magna exposed to narcotics and polar narcotics - aniline GSE29856: Daphnia magna exposed to narcotics and polar narcotics - 4-chloroaniline GSE29857: Daphnia magna exposed to narcotics and polar narcotics - 3,5-dichloroaniline GSE29858: Daphnia magna exposed to narcotics and polar narcotics - 2,3,4-trichloroaniline GSE29862: Daphnia magna exposed to narcotics and polar narcotics - ethanol GSE29864: Daphnia magna exposed to narcotics and polar narcotics - isopropanol GSE29867: Daphnia magna exposed to narcotics and polar narcotics - methanol Refer to individual Series

2012-02-01 | E-GEOD-29993 | biostudies-arrayexpress

Multigenerational DNA methylation responses to copper exposure in Daphnia: potential targets for epigenetic biomarkers?

Project description:Epigenetic mechanisms are moving to the forefront of environmental sciences, especially because environmentally induced epigenetic changes shape biological responses to contamination of chemicals. Moreover, such marks can be inherited by subsequent generations through epigenetic transgenerational inheritance, thus having long-term implications. In this work, we focused on Daphnia as a representative of the potentially threatened freshwater biota aiming to gain an insight on the involvement of epigenetic mechanisms in their response, eventually adaptation, to metal contamination. Copper induced DNA methylation changes, their potential transgenerational inheritance, and life-history traits were assessed. Organisms differing in their history of past exposure to copper were exposed to toxic levels of the element for one-generation (F0) and then monitored for three subsequent unexposed generations (F1, F2, and F3). Overall, methylation changes targeted important genes for counteracting the effects of metals and oxidative stress, including dynein light chain, ribosomal kinase and nuclear fragile X mental retardation-interacting protein. Also, contrasting overall and gene-specific methylation responses were observed in organisms differing in their history of exposure to copper, with different transgenerational methylation responses being also identified among the two groups, without apparent life-history costs. Taken together, these results demonstrate the capacity of copper to promote epigenetic transgenerational inheritance in a specific manner concerning past history of exposure, thereby supporting the potential of developing and incorporating epigenetic biomarkers in risk assessment frameworks.

2023-03-14 | GSE201140 | GEO

Transgenerational DNA methylation changes in Daphnia magna exposed to chronic gamma radiation

Project description:DNA methylation epigenetic changes were analysed in Daphnia magna exposed for 25-day to chronic gamma irradiation compared to unexposed controls. Generation F0 were exposed to 6.5 μGy/h or 41.3 mG/h and let recoverd until the F3 generation without exposures to ionizing radiations. DNA-methylation patterns were analysed by WGBS on the whole organismes at the generation F0, F2 and F3 in order to detect possible transmission of DNA methylation changes to the progeny.

2018-03-01 | GSE108426 | GEO

Long-term exposure of Daphnia magna to polystyrene microplastics induces changes in their proteome.

Project description:In the past years, the research focus on the effects of microplastics (MP) on aquatic organisms extended from marine systems towards freshwater systems. An important freshwater model organism in the MP field is the cladoceran Daphnia, which plays a central role in lacustrine ecosystems and has been established as a test organism in ecotoxicology. To investigate the effects of MP on Daphnia magna, we performed a chronic exposure experiment with polystyrene MP under strictly standardized conditions. Chronic exposure of D. magna to PS microparticles led to a significant reduction in body length and number of offspring. To shed light on underlying molecular mechanisms induced by microplastic ingestion in D. magna, we assessed the effects of PS-MP at the proteomic level.

2021-07-07 | PXD025108 | Pride

RNA-sequencing analysis of genetically identical female and male Daphnia magna with age

Project description:Comparison of female and male Daphnia magna gene expression with age. The sexes in Daphnia magna are genetically identical. The aim of this study was to identify possible differences in gene expression between genders with age.

2020-09-23 | GSE125466 | GEO

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