Project: Characterization of the fin methylome and transcriptome in three populations of the European sea bass (Dicentrarchus labrax)
Conditions: 5 months, starting from February 2025.
Laboratory: Center for Marine Biodiversity Exploitation and Conservation (MARBEC), Palavas-les-Flots, France (https://umr-marbec.fr/).
Contact:
IP: François Allal, françois(point)allal(arobase)ifremer(point)fr;
Post-doc: Nuria Sánchez-Baizán, nuria(point)sanchez(point)baizan(arobase)ifremer(point)fr
The UMR MARBEC produces and disseminates knowledge, trains scientists and provides expertise in the field of marine biodiversity and its uses, mainly in the Mediterranean and tropical marine ecosystems. You will be welcomed at the Ifremer experimental station in Palavas-les Flots, where research is mainly focused on the development of sustainable aquaculture, where around forty researchers, technicians and students work.
Context:
This master project will be part of EpiFishNess, a project dedicated to studying the epigenetic component of the FishNess ANR project (led by MARBEC). The FishNess ANR project aims to investigate phenotypic variation in robustness among European sea bass populations (Atlantic AT, West-Mediterranean WM, and East-Mediterranean EM) reared in captivity under different thermal regimes. FishNess evaluates robustness as the capacity to allocate energy toward growth, reproduction, and physiological performance, as well as the ability to cope with perturbations. Within this framework, EpiFishNess investigates the role of epigenetics in phenotypic plasticity. EpiFishNess will leverage the ongoing FishNess experiment to address three objectives: 1. Study epigenetic and gene expression differences among three sea bass populations exposed to the environmental regime representative of the East Mediterranean. 2. Identify potential population-specific aging rhythms and determine if they are affected by different temperature regimes through the construction of an individual-specific epigenetic clock. 3. Build a model integrating genomic and epigenetic data to predict which fish would be more robust in a particular environment. This research will contribute to better fisheries management and sustainable practices in aquaculture. Additionally, it will contribute to the understanding of genotype-environment interactions, local adaptation, and the impact of global warming on sea bass populations.
The master project will mainly contribute to the first objective of EpiFishNess, focusing on the study of epigenetic and gene expression differences among three sea bass populations reared in the East Mediterranean thermal regime.
Epigenetic marks are thought to play a role in local adaptation and short-term evolution. However, information about their effect in animal models is scarce, and it remains a topic of debate (1–3). Epigenetics encompasses mechanisms that cause chromosome-bound, heritable changes to gene expression that are not dependent on changes in the DNA sequence. It serves as a link integrating genomic and environmental information to regulate gene expression, contributing to phenotypic plasticity and thus to an organism's ability to respond to changing environments (4).
Among epigenetic mechanisms, DNA methylation is the most frequently studied due to its stability and relative ease of quantification using available technologies (5,6). Additionally, DNA methylation levels at specific loci in response to environmental stimuli and linked to phenotypes can be used as epigenetic biomarkers. These epigenetic marks can have diagnostic and prognostic value and hold great promise for fisheries management and aquaculture (7,8). Some environmentally-induced marks can be transmitted to subsequent generations (9), and recent evidence in the European sea bass suggests a cumulative effect of temperature on the epigenome at the multigenerational level (Sánchez-Baizán et al., In prep.).
Epigenetic marks are highly tissue-specific (10). Thus, we are investigating the methylome and transcriptome in three key tissues: the liver, which is central to metabolism and overall fitness of the fish; the muscle, a tissue related to growth; and the fin, which is in direct contact with the environment, ideal for studying responses to external stimuli. Importantly, fin samples can be obtained non-lethally, making them valuable for developing biomarkers and allowing repeated sampling without harming the fish.
Objective:
The objective of the masters’ project will be to investigate the methylome of the three populations of sea bass reared at the East Mediterranean environment. To do so, we will integrate this information with phenotypic data (fin shape, lesions/regeneration in the fin, body weight, body length, hepatosomatic index, gonad information, etc.). Additionally, transcriptomic data from the same tissue and individuals will be available. The main aim is to identify epigenetic or genetic markers associated to phenotypic traits related to fish robustness.
Materials available:
All data required for this project is already available. We sampled the fish in March 2023 and we prepared 12 libraries (pools of 4 individuals each) for the analysis of the whole methylome through the enzymatic methyl sequencing technique (11) (~57 Gb). Similarly, we prepared 12 libraries from the same individuals and from the same part of tissue for RNA -sequencing (~35 Gb). In addition, we recorded several phenotypic data during the sampling such as biometric data of different body parts and we took photos of all the individuals (~2 Gb). The bioinformatic analysis of the data has already been done, but some further analysis will be required. The interested applicant will have the opportunity to participate in other samplings related to FishNess project in order to get practical experience and also, he/she will be assisted with the bioinformatic and statistical analysis as well as the production of the report.
Planning:
Feb Mar Apr May June getting familiar with RNA seq and methylome data
Statistical analysis to identify epi- and/or genetic markers correction of main figures and writing of the report
Skills required:
• A good level of English is required
• Knowledge on animal biology, aquaculture, statistics, and programming in R Software. Ideally, some knowledge on bioinformatics or on the analysis of RNA-seq data would be desired.
Contact:
IP: François Allal, françois(point)allal(arobase)ifremer(point)fr;
Post-doc: Nuria Sánchez-Baizán, nuria(point)sanchez(point)baizan(arobase)ifremer(point)fr
References:
1. Schmid MW, Heichinger C, Coman Schmid D, Guthörl D, Gagliardini V, Bruggmann R, et al. Contribution of epigenetic variation to adaptation in Arabidopsis. Nat Commun. 25 oct 2018;9(1):4446.
2. Herden J, Eckert S, Stift M, Joshi J, van Kleunen M. No evidence for local adaptation and an epigenetic underpinning in native and non‐native ruderal plant species in Germany. Ecol Evol. 6 août 2019;9(17):9412‑26.
3. Zhang X, Guo R, Shen R, Landis JB, Jiang Q, Liu F, et al. The genomic and epigenetic footprint of local adaptation to variable climates in kiwifruit. Hortic Res. 4 avr 2023;10(4):uhad031.
4. Deans C, Maggert KA. What Do You Mean, “Epigenetic”? Genetics. 1 avr 2015;199(4):887‑96.
5. Bock C. Epigenetic biomarker development. Epigenomics. oct 2009;1(1):99‑110.
6. Piferrer F, Anastasiadi D, Valdivieso A, Sánchez-Baizán N, Moraleda-Prados J, Ribas L. The Model of the Conserved Epigenetic Regulation of Sex. Front Genet. 26 sept 2019;10:857.
7. Valdivieso A, Sánchez-Baizán N, Mitrizakis N, Papandroulakis N, Piferrer F. Development of epigenetic biomarkers with diagnostic and prognostic value to assess the lasting effects of early temperature changes in farmed fish. Aquaculture. 30 janv 2023;563:738918.
8. Piferrer F. Epigenetics in Aquaculture. In: Epigenetics in Aquaculture [Internet]. John Wiley & Sons, Ltd; 2023 [cité 26 sept 2024]. p. 451‑63. Disponible sur: https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119821946.ch20
9. Wang X, Bhandari RK. DNA methylation dynamics during epigenetic reprogramming of medaka embryo. Epigenetics. juin 2019;14(6):611‑22.
10. Gutierrez-Arcelus M, Ongen H, Lappalainen T, Montgomery SB, Buil A, Yurovsky A, et al. Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing. PLOS Genet. 29 janv 2015;11(1):e1004958.
11. Vaisvila R, Ponnaluri VKC, Sun Z, Langhorst BW, Saleh L, Guan S, et al. Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. Genome Res. juill 2021;31(7):1280‑9.