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Epigenomic of the stress response in the European sea bass

ABSTRACT: Understanding the molecular basis of stress is crucial in biology and of long standing interest in fish science. We tackled this question by modifying the epiGBS (epiGenotyping By sequencing) technique to screen for cytosine methylation and explore the genome-wide epigenomic response to a three months repeated acute stress challenge in the European sea bass (Dicentrarchus labrax). Following a minimally invasive sampling using nucleated red blood cells (RBCs), our modified epiGBS protocol retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% for unique best hits. Sequencing reads were shown to map across all linkage groups (LGs) of sea bass. A total of 47,983 CpG coordinates with a minimum 30X read depth was retained for differential methylation analysis between pre- and post-stress fish. A strong family effect was demonstrated, and fifty-seven distinct differentially methylated cytosines (DMCs) distributed on 17 of 24 LGs were found between RBCs of pre- and post-stress individuals. Twelve of them were located in intergenic regions, one in a repeated element; and forty four in gene bodies. Overall, DMCs were found inside or in the vicinity of 51 distinct genes shown previously to be related to stress. Thirty-eight of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences.

ORGANISM(S): Dicentrarchus labrax

PROVIDER: GSE156637 | GEO | 2020/10/30

REPOSITORIES: GEO

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Genome scale epigenomic analysis of response to acute stress in the European sea bass

Project description:Understanding the molecular basis of stress is crucial in biology and of long standing interest in fish science. We tackled this question by modifying the epiGBS (epiGenotyping By sequencing) technique to screen for cytosine methylation and explore the genome-wide epigenomic response to a three months repeated acute stress challenge in the European sea bass (Dicentrarchus labrax). Following a minimally invasive sampling using nucleated red blood cells (RBCs), our modified epiGBS protocol retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% for unique best hits. Sequencing reads were shown to map across all linkage groups (LGs) of sea bass. A total of 47,983 CpG coordinates with a minimum 30X read depth was retained for differential methylation analysis between pre- and post-stress fish. A strong family effect was demonstrated, and fifty-seven distinct differentially methylated cytosines (DMCs) distributed on 17 of 24 LGs were found between RBCs of pre- and post-stress individuals. Twelve of them were located in intergenic regions, one in a repeated element; and forty four in gene bodies. Overall, DMCs were found inside or in the vicinity of 51 distinct genes shown previously to be related to stress. Thirty-eight of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences.

2020-07-07 | GSE153838 | GEO

Effects of the total replacement of fish meal and fish oil with plant protein and oil sources on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) sub-families exhibiting different growth potentials on an all plant-based diet

2011-09-01 | GSE27649 | GEO

Project description:Comparison of the hepatic transcriptomes for two half-sib-families of European sea bass fed on vegetable and fish diet. These two half-sib-families exhibit similar growth on fish diet while significantly different on vegetable diet. The aim of the study is to point out the large panel of metabolic and physiological effects induced by total substitution of both fish meal and fish oil in the diets of European sea bass and to reveal physiological characteristics associated to the two half-sib-families. Fish from both two half-sib-families (G and g) were fed a a fish diet (FD) or a vegetable diet (VD) diet for 9 months. Five to eight independent experiments were performed for each experimental groups (G-FD; G-VD; g-FD; g-VD) using different fishes for each experiment.

2011-08-31 | E-GEOD-27649 | biostudies-arrayexpress

Characterization of the European sea bass (Dicentrarchus labrax) gonadal transcriptome during different stages of development

Project description:We have further tested and validated a reproduction-enriched microarray designed specifically for European sea bass providing a reliable tool to study gene expression patterns in this fish species. Results obtained by using this platform helped to increase our knowledge in the gene cascade of sex differentiation and give evidence of the complexity of the molecular processes. We described the gene expression profile of genes and pathways required to differentiate bipotential tissue to either an ovary or testis providing a deep transcriptomic analysis in the developing gonads. Resulting data may help to improve sex control in fish culture particularly in the European sea bass

2019-12-01 | GSE115841 | GEO

The Gene expression gradient through the intestine tract of European Sea Bass (Dicentrarchus labrax)

Project description:A custom high density oligo-microarray (8 x 15K) was designed and printed by means of the eArray web tool (Agilent) to analyze the transcriptome of the three intestinal sections of Euroipan sea bass (Dicentrarchus labrax). Naïve stock juveniles sea bass, maintained under intensive rearing conditions in the indoor experimental facilities of IATS, were sampled after overnight fasting for anterior, middle and posterior sections of intestine. The array comprised 60-oligomer sequences for 14,147 different sea bass annotated sequences. Total RNA (150ng) from individual fish were labelled with cyanine 3-CTP and 1,000ng of each labelled cRNA were hybridized to microarray slides. Analysis of the scanned data, including principal component analysis and unpaired t-test with Benjamini-Hochberg multiple testing correction, was carried out with GeneSpring GX software (Agilent). Pathway analysis of differentially expressed sequences was performed using the Ingenuity Pathway Analysis (IPA) software.

2017-07-08 | GSE59240 | GEO

Dataset of the proteome profiles of sea bass (Dicentrarchus labrax) skin-scale exposed to estradiol and fluoxetine

Project description:Contamination of aquatic ecosystems with anthropogenic pollutants, including pharmaceutical drugs, is a major concern worldwide. Fish are particularly at risk of exposure to pollutants but their impacts on mineralized fish tissues, particularly the scales that form a barrier between the fish and the environment, are poorly understood. The proteome data here presented support the findings reported in the associated research article “Disruption of the sea bass (Dicentrarchus labrax) skin-scale by estradiol and fluoxetine, an emerging pollutant”. Juvenile sea basses were exposed by intraperitoneal injections to: a) the antidepressant fluoxetine (FLX), a widely prescribed psychotropic drug and an emerging pollutant; b) the natural estrogen 17β-estradiol (E2) and c) coconut oil alone (control). The scale proteome profiles of fish exposed to these compounds for 5 days were analysed by the quantitative label-free proteomics technology SWATH-MS (Sequential Windowed data-independent Acquisition of the Total High-resolution-Mass Spectra). LC-MS data from pooled protein extracts from the scales of all experimental groups were acquired using information-dependent acquisition (IDA), which allowed the identification of 1,254 proteins through searches against the sea bass genome database. 715 proteins were confidently quantified by SWATH acquisition, from which 213 proteins had modified levels (p<0.05) between E2- or FLX-exposed fish and control. The main biological processes and KEGG pathways affected by E2 or FLX treatments were identified using Cytoscape/ClueGO enrichment analyses.

2022-01-11 | PXD020983 | Pride

An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax) I

Project description:A sea bass oligo microarray platform was used to profile gene expression in whole heads of 38 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) prognathous individuals, and ii) normal individuals were analyzed. For each condition, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of five (5) heads.

2017-02-12 | GSE85052 | GEO

An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax) II

2017-02-12 | GSE85054 | GEO

Comparison of gene expression profile between 58 days-old prognatous sea bass jaws and control ones

Project description:A sea bass oligo microarray platform was used to profile gene expression in mandibles of 58 days-old sea bass affected by prognathism, a skeletal malformation that strongly affects sea bass production. Two different conditions: i) protruding jaws, and ii) normal jaws were used for gene expression analysis. For each condition, total RNA was extracted from four (4) independent biological replicates, each consisting of pools of five (5) jaws. Statistical analysis with SAM (Significance Analysis of Microarray) identified 333 probes (corresponding to 242 unique transcripts) significantly down-regulated in deformed individuals compared to normal ones.

2010-10-22 | GSE19001 | GEO

Study of the onset of puberty in the European sea bass

Project description:Pubertal development in males starts with the onset of spermatogenesis that implies the division of primary spermatogonia and their subsequent entry into meiosis. Whole genome microarray expression profile was used as a means to explore the molecular basis underlying the onset of pubertal development in sea bass. The present study is aimed at the characterization of the expression of genes involved in the onset of spermatogenesis in the European sea bass. The study is focused on the first stages of the process including the appearance of spermatocytes and thus the first meiotic divisions. The transcriptomic study using a sea bass-specific microarray resulted in a number of genes differentially expressed during the onset of spermatogenesis. Among those, genes involved in cell-cycle progression, microtubule assembly during meiosis or retinoic acid signaling pathway indicating that they can be used as potential molecular markers for the onset of spermatogenesis in sea bass.

2017-06-23 | GSE47400 | GEO

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