Transcriptional response to embryonic PCB exposure in 8 killifish populations
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ABSTRACT:
PROVIDER: PRJNA658029 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12475500.fastq.gz | Fastqsanger.gz | |||
| SRR12475500_1.fastq.gz | Fastqsanger.gz | |||
| SRR12475500_2.fastq.gz | Fastqsanger.gz | |||
| SRR12475501.fastq.gz | Fastqsanger.gz | |||
| SRR12475501_1.fastq.gz | Fastqsanger.gz |
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Project description:Embryos from 8 populations of killifish, four with evolved tolerances, were exposed to PCB-126. Approximately 5 replicate embryos per treatment/control were sequenced. Desensitization of aryl hydrocarbon receptor signaling to PCB-126 is found in all four populations with evolved pollution tolerance, and represents the strongest transcriptional difference between tolerant and sensitive populations.
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Project description:RNA from PCB-126 exposed 10 days post-fertilization (dpf) embryos were sequenced to characterize the chemical exposure response of killifish from a PCB-resistant population (NBH, New Bedford Harbor, MA, Superfund site) as compared to a reference (SC, Scorton Creek, MA) population. Since the genome sequence was not available, we also performed shot-gun sequencing of RNA from 1-15 dpf embryos sampled every day from both populations to serve as a transcriptome assembly. The results suggest that the NBH fish possess a gene regulatory defect that is not limited to a few target genes. We detected multiple genes that were differentially expressed in these two populations. This study was the first application of pyrosequencing technology to combine transcriptome characterization and gene expression profiling in a marine animal.
2016-09-09 | GSE86593 | GEO
Project description:Diapause is a reversible developmental arrest faced by many organisms in harsh environments. Annual killifish present this mechanism in three possible stages of development. Killifish are freshwater teleosts from Africa and America that live in ephemeral ponds, which dry up in the dry season. The juvenile and adult populations die, and the embryos remain buried in the bottom mud until the next rainy season. Thus, species survival is entirely embryo-dependent, and they are perhaps the most remarkable extremophile organisms among vertebrates. The aim of the present study was to gather information about embryonic diapauses with the use of a “shotgun” proteomics approach in diapause III and prehatching Austrolebias charrua embryos. Our results provide insight into the molecular mechanisms of diapause III. We detected a diapause-dependent change in a large group of proteins involved in different functions, such as metabolic pathways and stress tolerance, as well as proteins related to DNA repair and epigenetic modifications. Furthermore, we observed a diapauseassociated switch in cytoskeletal proteins. This first glance into global protein expression differences between prehatching and diapause III could provide clues regarding the induction/maintenance of this developmental arrest in A. charrua embryos. There appears to be no single mechanism underlying diapause and the present data expand our knowledge of the molecular basis of diapause regulation. This information will be useful for future comparative approaches among different diapauses in annual killifish and/or other organisms that experience developmental arrest.
2021-05-12 | PXD025196 | Pride
Project description:Killifish (Fundulus heteroclitus) inhabiting the New Bedford Harbor (NBH) Superfund Site have evolved resistance to the toxic and biochemical effects of non-ortho (dioxin-like) polychlorinated biphenyls (DL-PCBs) and other compounds that act via the aryl hydrocarbon receptor (AHR) signaling pathway. However, the majority of PCBs in NBH are ortho-substituted (non-DL) PCBs (o-PCBs), and the impacts of these o-PCBs on fish populations are not well understood. To determine whether the NBH killifish population has adapted to o-PCBs, we performed a series of experiments involving exposure to killifish embryos and adults from NBH and a reference site (Scorton Creek; SC) to 2,2’,4,4’,5,5’-hexachlorobiphenyl (PCB-153), a model o-PCB. PCB-153 was not acutely embryotoxic to developing F2 killifish embryos (SC or NBH) at concentrations up to 28 µM. RNA-seq showed that SC embryos exposed to PCB-153 (28 µM for 6 hr at 10 days post fertilization) had changes in the expression of genes involved in glucose homeostasis. However, NBH embryos were much less sensitive to these effects of PCB-153. When adult killifish from SC and NBH were exposed to PCB-153 (20 mg/kg) and sampled 3 days later for gene expression, many more genes were affected in forebrains of SC fish than in NBH fish, in a sex-specific manner. Together, these results demonstrate that NBH killifish have evolved reduced sensitivity to o-PCBs, suggesting complex adaptation to chemical mixtures at a Superfund site.
2018-06-16 | GSE115863 | GEO
Project description:The Atlantic killifish (Fundulus heteroclitus) is an ideal model species to study physiological and toxicological adaptations to stressors. Killifish inhabiting the PCB-contaminated Superfund site in New Bedford Harbor, MA (NBH) have evolved resistance to toxicity and activation of the aryl hydrocarbon receptor (AHR) signaling pathway after exposure to PCBs and other AHR agonists. Until recently, a lack of genomic information has limited efforts to understand the molecular mechanisms underlying environmental adaptation to stressors. The advent of high throughput sequencing has facilitated an unbiased assessment of coding as well as non-coding RNAs in any species of interest. Among non-coding RNAs, microRNAs (miRNAs) are important regulators of gene expression and play crucial roles in development and physiology. The objective of this study is to catalog the miRNAs in killifish and determine their expression patterns in the embryos from contaminated (NBH) and pristine (Scorton Creek, MA (SC)) sites. Embryos from NBH and SC were collected daily from 1 to 15 days post-fertilization and RNA from pooled samples from each site was sequenced using SOLiD sequencing. We obtained 7.5 and 11 million raw reads from pooled SC and NBH samples, respectively. Analysis of the sequencing data identified 216 conserved mature miRNA sequences that are expressed during development. Using the draft killifish genome, we retrieved the miRNA precursor sequences. Based on the capacity of these putative precursor sequences to form the characteristic hairpin loop (assessed using RNAfold), we identified 197 conserved miRNA sequences in the genome.
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Project description:This is a common-garden experiment comparing the transcriptional response to multiple doses of PCB-126 among multiple populations of the killifish Fundulus heteroclitus
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Project description:The effects exerted by three mixtures of Polychlorinated Biphenyls (PCB), one featuring dioxin-like (DL) and two featuring non dioxin-like (NDL) congeners, on human fetal corpora cavernosa cells representative of a major male endocrine-sensitive organ, have been evaluated by gene expression profiling. PCB congeners concentrations used were derived from human internal exposure data to explore the impact of the adult body burden on a fetal tissue. Cell exposure were performed for 72h mimicking a chronic exposure. Experiment conditions: control, three treatments with PCB-Mix1, PCB-Mix2 or PCB-Mix3. Biological replicates: 3 control replicates, 3 replicates per treatment. Technical replica: 2 (dye swap) per biological replica. Direct comparison design (control vs treated samples) in 12/16 arrays (biological replicates 1 and 2); Loop design in 4/16 arrays (biological replicate 3).
2010-11-09 | E-GEOD-25193 | biostudies-arrayexpress
Project description:Exposure to Polychlorobiphenyls (PCBs) is known to cause serious health effects in human but the gene expression profiles leading to development of differnet diseases and disorders are not fully understood. The knowledge of global gene expression will help us to devlop early disease or disorder biomarkers for PCB induced health effects. We used microarrays to detail the global gene expression profile underlying the effects of PCB 138 exposure to human PBMC leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes. Keywords: PCB 138 Exposures
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Project description:Polychlorinated biphenyls (PCBs) are developmental neurotoxicants implicated as environmental risk factors for neurodevelopmental disorders (NDD). We examined the effects of prenatal exposure to a human-relevant mixture of PCBs on the DNA methylation profiles of fetal mouse brain and placenta. We found thousands of differentially methylated regions (DMRs) distinguishing placentas and brains from PCB-exposed embryos from sex-matched vehicle controls. In both placenta and brain, PCB-associated DMRs were enriched for functions related to neurodevelopment and cellular signaling and enriched within regions of bivalent chromatin. The placenta and brain PCB DMRs overlapped significantly and mapped to a shared subset of genes enriched for Wnt signaling, Slit/Robo signaling, and genes differentially expressed in NDD models. PBC DMRs also significantly overlapped with DMRs from the brains of humans with Rett syndrome and Dup15q syndrome. These results demonstrate that placenta can be used as a surrogate for embryonic brain DNA methylation changes relevant to an NDD.
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Project description:Polychlorinated biphenyls (PCBs) are developmental neurotoxicants implicated as environmental risk factors for neurodevelopmental disorders (NDD). We examined the effects of prenatal exposure to a human-relevant mixture of PCBs on the DNA methylation profiles of fetal mouse brain and placenta. We found thousands of differentially methylated regions (DMRs) distinguishing placentas and brains from PCB-exposed embryos from sex-matched vehicle controls. In both placenta and brain, PCB-associated DMRs were enriched for functions related to neurodevelopment and cellular signaling and enriched within regions of bivalent chromatin. The placenta and brain PCB DMRs overlapped significantly and mapped to a shared subset of genes enriched for Wnt signaling, Slit/Robo signaling, and genes differentially expressed in NDD models. PBC DMRs also significantly overlapped with DMRs from the brains of humans with Rett syndrome and Dup15q syndrome. These results demonstrate that placenta can be used as a surrogate for embryonic brain DNA methylation changes relevant to an NDD.
2022-03-03 | GSE171016 | GEO