Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.)

Abstract

Background In fish, minimally invasive blood sampling is widely used to monitor physiological stress with blood plasma biomarkers. As fish blood cells are nucleated, they might be a source a potential new markers derived from ‘omics technologies. We modified the epiGBS (epiGenotyping By Sequencing) technique to explore changes in genome-wide cytosine methylation in the red blood cells (RBCs) of challenged European sea bass (Dicentrarchus labrax), a species widely studied in both natural and farmed environments. Results We retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% (unique best hits). Minor changes in RBC methylome appeared to manifest after the challenge test and a family-effect was detected. Only fifty-seven differentially methylated cytosines (DMCs) close to 51 distinct genes distributed on 17 of 24 linkage groups (LGs) were detected between RBCs of pre- and post-challenge individuals. Thirty-seven of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences. While further investigation remains necessary, few DMC-related genes associated to the Brain Derived Neurotrophic Factor, a protein that favors stress adaptation and fear memory, appear relevant to integrate a centrally produced stress response in RBCs. Conclusion Our modified epiGBS protocol was powerful to analyze patterns of cytosine methylation in RBCs of D. labrax and to evaluate the impact of a challenge using minimally invasive blood samples. This study is the first approximation to identify epigenetic biomarkers of exposure to stress in fish.

Age estimation in fishes using epigenetic clocks: Applications to fisheries management and conservation biology

“…Lastly, the species considered should come from different geographic locations. Epigenetic modifications have a strong underlying genetic basis and, in addition, can be influenced by changes in the environment such as by temperature changes (Anastasiadi et al, 2018), diet composition (Dhanasiri et al, 2020) and stress (Krick et al, 2021). Therefore, it is possible to find differences among different populations of the same species.…”

Genomic imprinting-like monoallelic paternal expression determines sex of channel catfish

“…In European sea bass, juvenile males have doubled DNA methylation levels in the promoter of gonadal aromatase (cyp19a) as compared to females; when exposed to high temperature, DNA methylation in the promoter region of gonadal aromatase cyp19a was increased in females (48). Recently, the epigenetic control of key genes for sexual development (cyp19a1a and dmrt1) in European sea bass has been reported (51). Considering the evolutionary position of channel catfish as a lower teleost, it is possible that such a sex determination mechanism could be operating in other lower vertebrates as well, especially those whose sex is highly vulnerable to environmental factors, such as temperature, which could function through their effects on genome methylation (28,48,50,(52)(53)(54).…”

Development of epigenetic biomarkers with diagnostic and prognostic value to assess the lasting effects of early temperature changes in farmed fish

“…However another environmental factor, with detrimental effects on European sea bass development is rearing density (Sammouth et al, 2009), albeit without effects on sex ratio (Saillant et al, 2003) as temperature does. In an experiment with 6 month-old European sea bass exposed to short intervals of acute density stress, 57 DMCs in 51 distinct genes measured in blood samples were identified (Krick et al, 2021). Interestingly, among these 51 genes, two genes were also present in our list of genes with DMCs in three tissues: roundabout homolog 2-like (robo3) in 20 • C vs. 17 • C and zinc finger matrin-type 4b (smat4) in 14 • C vs. 17 • C. These two genes seem to be involved in behavior linked with stress conditions (Rey et al, 2013).…”

“…Of note, epigenetic biomarkers not only can have diagnostic but also prognostic value, since sometimes epigenetic changes appear long before gene expression or other phenotypic changes become apparent (Costa-Pinheiro et al, 2015). In the European sea bass, DNA methylation-based biomarkers have already been developed to predict sex (Anastasiadi et al, 2018), assess the early stages of domestication (Anastasiadi and Piferrer, 2019b), determine biological age (Anastasiadi and Piferrer, 2019a), assess the consequences of heat waves (Anastasiadi et al, 2021), and to evaluate the stress response associated with rearing density (Krick et al, 2021). However, and to the best of our knowledge, there are no epigenetic biomarkers in the European sea bass or, for that matter, in any other farmed fish species, that can be used to link the temperature regime during early stages of development with subsequent aquaculture performance.…”