Roberto Carlos ARREDONDO-ESPINOZA

Previous BOREA member

Research topic: Chromatin Structure, Environment and Methylation of Nucleic Acids in the Oyster (SCHEMAh). 

The SCHEMAh project has been developed under different questions based on the phenotypic plasticity of the oyster Crassostrea gigas. The phenotypic plasticity of this organism has been well studied highlighting the physiological response as a resilient adjustment to environmental changes. For this reason, the C. gigas oyster is considered a model organism for research, including transcriptomic profiling (gene expression patterns), epigenetics and physiological behaviour.

In the Normandy region, the C. gigas oyster is the most important shellfish resource and its ecology makes it particularly exposed to environmental changes (tides, seasons, global change), which forces the organisms to develop physiological responses through different mechanisms mediated by gene expression. Currently, studies about the structuring of genetic material have suggested its importance for gene expression, including the behavior of chromatin structure under the influence of nucleic acid methylation. Indeed, this prevalent epigenetic mechanism promotes the chromatin condensation (5mC-DNA methylation) and allows the extra chromosome locking (m6A-RNA methylation) in mammals. Nevertheless, although if 5mC-DNA and m6A-RNA are present in C. gigas and despite triploid oysters are fit and can be fertile, the influence of environmental factors on nucleic acid methylation and chromatin structure in the oyster remains totally unknown to date.

In this context, the SCHEMAh project aims to answer the following questions:

"How does the modification of gene expression in C. gigas allow an appropriate physiological response to environmental changes?

"How does the environment control the structure of the genetic material via nucleic acid methylation in the oyster model and thus the expression of the genes that enable adaptation?

"How are DNA methylation (5mC) and chromatin structure related?

"How can the existence of m6A-methylated non-coding RNAs (m6A-carRNAs) in triploid oysters compensate for their aberrant chromosomal dosage?

 

My post-doctorate is part of the development and exploitation of innovative molecular approaches within the SCHEMAh project: (Chromatin Accessibility Assay, ATAC-seq, Nanopore sequencing). I will notably perform bioinformatics analyses of the data generated by the high-throughput sequencing methodologies undertaken within the project (RNA-seq, Methyl-seq, m6A-RNA-seq, ATAC-seq).

The pioneer fundamental knowledge brought by this project constitute a strong asset to understand the adaptation of the oyster C. gigas, a model of major scientific interest and a key component of the Normandy coastal ecosystem, and more generally of species, towards the global change.

 

The entire Post-Doc position is covered and supported by the Conseil Régional de Normandie (RIN Recherche Emergent 'SCHEMAh' - convention 00110890-21 E 05080 from 01/11/2021 to 30/04/2024).