Functional role of epitranscriptomic regulation in the Pacific oyster Crassostrea gigas

Epitranscriptomic modifications, such as RNA methylation (particularly m⁶A), represent an additional layer of gene expression regulation. They are involved in key cellular processes including alternative splicing, translation, and RNA stability, especially in Mammals and Ecdysozoans. In Mammals, for instance, m⁶A plays a central role in the inactivation of one X chromosome in females by promoting the binding of a methylated non-coding RNA to chromatin, leading to chromosome compaction and silencing.

In the Pacific oyster, previous studies have shown that RNA methylation correlates with gene expression during early development. However, the specific functions of this regulation remain largely unknown in Lophotrochozoans, a group notable for its remarkable biodiversity.

The aim of my PhD project is to explore the roles of epitranscriptomic regulation during early development as well as in adults, in the context of potential chromatin dosage compensation. We will also investigate methylation-prone sequence motifs as proxies for actual methylation and perform comparative analyses in a broad phylogenetic framework.

The main research questions of this project are:

• Objective 1: What is the role of epitranscriptomic regulation during embryonic and larval development in oysters?
• Objective 2: Do triploid oysters capable of reproduction exhibit chromatin dosage compensation mediated by non-coding RNA methylation (m⁶A-carRNA), as seen in X-chromosome inactivation in female mammals?
• Objective 3: Can methylation-prone sequence motifs serve as reliable predictors of actual methylation, and what insights can be gained from evolutionary comparisons?

This research will advance our understanding of epitranscriptomic regulation in Lophotrochozoans within an evolutionary context.