Ontology highlight
ABSTRACT:
PROVIDER: PRJNA322734 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3586040.fastq.gz | Fastqsanger.gz | |||
| SRR3586041.fastq.gz | Fastqsanger.gz | |||
| SRR3586042.fastq.gz | Fastqsanger.gz | |||
| SRR3586043.fastq.gz | Fastqsanger.gz | |||
| SRR3586044.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For non-model organisms with adaptive key-innovations, patterns of regulatory evolution have been predominantly limited to targeted sequence-based analyses. Chromatin-immunoprecipitation with high-throughput sequencing (ChIP-seq) is a technology that has only been used in genetic model systems and is a powerful experimental tool to screen for active cis-regulatory elements. Here, we show that it can also be used in ecological model systems and permits genome-wide functional exploration of cis-regulatory elements. As a proof of concept, we use ChIP-seq technology in adult fin tissue of the cichlid fish Oreochromis niloticus to map active promoter elements, as indicated by occupancy of trimethylated Histone H3 Lysine 4 (H3K4me3). The fact that cichlids are one of the most phenotypically diverse and species-rich families of vertebrates could make them a perfect model system for the further in-depth analysis of the evolution of transcriptional regulation. examination of H3K4me3 in adult fin tissue of the Nile tilapia (Oreochromis niloticus)
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Project description:The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal, middle and distal adult fin tissue of hypothyroid zebrafish, with euthyroid sibling fish as control.
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Project description:Our main objectives were: 1) to test whether the caudal fin may be used to detect the effects of pollutant exposure by means of DNA microarray; 2) to test whether the fin may be used to detect the effects of pollutants in wild contaminated fish; 3) to investigate the mechanisms of toxicity for Cd metal. Detecting and unraveling specific effects of contaminants in a multi-stress field context remain a major challenge in ecotoxicology. The aim of this study was to apply a previously developed DNA microarray comprising 1000 candidate genes on caudal fin clips in order to assess the usefulness of a non-invasive method in ecotoxicogenomic studies in the European eel. Fin gene expression patterns of eels exposed in laboratory to Cd or a PCBs mixture were compared to test whether fin clips may be used to detect effects of these contaminants. Then, gene transcription profiles of wild fish from 3 sampling sites with differing contamination levels were compared to experimental exposures to test whether fin could detect and unravel the in situ effects of these contaminants. Also, transcriptomic profiles from liver and caudal fin of eels experimentally exposed to Cd were compared to test whether fins may be used to investigate the toxicity mechanisms of this metal. Our results showed distinct fin transcription profiles in response to Cd or PCBs exposure. In addition, the transcription profiles of eels from the most contaminated site clustered with the laboratory-exposed fish. Finally, gene transcription patterns from caudal fin and liver in Cd-exposed eels showed significant differences between the two organs and only 16 common genes were identified. Many of these genes were found to be involved in tissue development and in epigenetic mechanisms. This study thus demonstrates the applicability and usefulness of performing gene transcription assays on non-invasive tissue sampling in order to assess the effect of Cd and PCBs on the transcriptome of fish.
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