Daphnia gene expression after copper exposure
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ABSTRACT:
PROVIDER: PRJEB28650 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2796170_1.fastq.gz | Fastqsanger.gz | |||
| ERR2796170_2.fastq.gz | Fastqsanger.gz | |||
| ERR2796180_1.fastq.gz | Fastqsanger.gz | |||
| ERR2796180_2.fastq.gz | Fastqsanger.gz | |||
| ERR2796190_1.fastq.gz | Fastqsanger.gz |
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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.
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Project description:Daphnia (Daphnia pulex) is a small planktonic crustacean and a key constituent of aquatic ecosystems. It is commonly used as a model organism for studying environmental toxic challenges. In the past decade, a Daphnia genomic information and proteomic dataset has been developed. This dataset has expanded the opportunity to relate toxicological effects with “Daphnia proteomics” as it integrates proteomic knowledge in Daphnia, those approach will provide greater insights for toxicological research. In order to exploit Daphnia for ecotoxicological research, information on the post-translational modification (PTM) of proteins is necessary as this is a critical regulator of biological processes. Acetylation of lysine (Kac) is a reversible and highly regulated PTM that is associated with diverse biological functions. However, a comprehensive description of Kac in Daphnia is not yet available. Here, to understand the cellular distribution of lysine acetylation in Daphnia, we identified 98 acetylation sites in 65 proteins by immunoprecipitation using an anti-acetyllysine antibody and an liquid chromatography system supported by mass spectroscopy. We identified 28 acetylated sites connected with metabolic proteins and 6 acetylated enzymes associated with the TCA cycle in Daphnia. From GO and KEGG enrichment analyses, we showed that Kac in D. pulex is highly enriched in proteins associated with metabolic processes. Our data provide the first global analysis of lysine acetylation in D. pulex. The expanded proteomic dataset will be an important resource for the functional analysis of Kac in D. pulex and it will be nice to have a first step done using a promising future model organism.
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Project description:This SuperSeries is composed of the following subset Series: GSE25841: Evolutionary Diversification of Duplicated Genes; Experiment A GSE25843: Evolutionary Diversification of Duplicated Genes; Experiments B-I, M-P GSE25845: Evolutionary Diversification of Duplicated Genes; Experiments B-I GSE25850: Evolutionary Diversification of Duplicated Genes; Experiment J GSE25851: Evolutionary Diversification of Duplicated Genes; Experiment L, K GSE25852: Empirical Annotation of the Daphnia pulex genome; Experiment B GSE25855: Empirical Annotation of the Daphnia pulex genome; Experiment A GSE25856: Empirical Annotation of the Daphnia pulex genome; Experiment C Refer to individual Series
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Project description:Over the past decade, significant advances have been made to unravel molecular mechanisms of stress response in different ecotoxicological model species. Within this study, we focus on population level transcriptomic responses of a natural population of Daphnia magna Straus, (1820), to heavy metals. We aim to characterize the population level transcriptomic responses, which include standing genetic variation, and improve our understanding on how populations respond to environmental stress at a molecular level. We studied population level responses to two heavy metals, copper and arsenic, and their binary mixture across time. Transcriptomic patterns identified significantly regulated gene families and genes at the population level including cuticle proteins and resilins. Furthermore, some of these differentially regulated gene families, such as cuticle proteins, were also significantly enriched for genetic variations including SNPs and MNPs. In general, genetic variation was observed in specific gene families, many of which are known to be involved in stress response. Overall, our results indicate that molecular stress responses can be identified within natural populations and that linking molecular mechanisms with genetic variation at the population level could contribute significantly to adverse outcome frameworks.
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Project description:Multigenerational DNA methylation responses to copper exposure in Daphnia: potential targets for epigenetic biomarkers?
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Project description:We report the application of CAGE (Cap Analysis of Gene Expression) on collections of Daphnia pulex individuals representing three major developmental states. This submission comes from a project of Michael Lynch and was funded by a grant from the National Institutes of Health entitled 'Population Genomics of Daphnia pulex' (Project Number: 1R01GM101672-01A1).
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Project description:Whole-genome sequencing for Daphnia pulex of lineages in Japan
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Project description:Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of non-lineage specific genes was conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families. Whole transcriptome dual color arrays were used to discover differentially expressed genes following sub-lethal exposure to five cyanobacteria in D. pulex. RNA was isolated from eight independent and concurrently replicated exposures of Daphnia to control and five cyanobacteria conditions. RNA was hybridized to microarrays using a standard, control vs. treated design that included dye swaps. Cyanobacteria were Anabaena (ANA), Aphanizomenon (Aph), Cylindrospermopsis (Cyl), Nodularia (Nod) and Oscillatoria (Osl).
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