CD4+ T cells protect vertebrates from many endogenous and exogenous menaces, including tumor cells, viruses, bacteria and parasites. Their efficacy is derived from their ability to develop specific phenotypes and functions in response to these threats. Following activation, naïve CD4+ T cells differentiate into distinct T helper (Th) lymphocyte lineages, such as Th1, Th2, Th17 and regulatory T cells (Treg), each characterized by specific gene expression programs. Epigenetic pathways, including histone post-translational modifications, DNA methylation, and long non-coding RNAs, have been shown to modulate the gene expression programs of these Th cell subsets.

However, a still little-explored regulatory mechanism is emerging: epitranscriptomics, which studies the biochemical modifications of RNAs. These RNA modifications or epitranscriptomic marks are present across various RNA types, including messenger RNAs (mRNA) and transfer RNAs (tRNA), and exert control over processes like RNA splicing, maturation and degradation. Similar to histone modifications, these epitranscriptomics marks are deposited by enzymes termed “writers”, eliminated by “erasers”, and recognized by “readers”, which are associated with specific functions. Over 150 such modifications have been identified, including N6-methyladenosine (m6A), 5-methylcytosine (m5C) and 7-méthylguanosine (m7G) modifications. Recent research has highlighted the role of METTL3 enzyme, which deposits m6A mark, in CD4+ T cells activation and differentiation.

Despite these findings, the functions of most other epitranscriptomic enzymes have not yet been studied in the biology of T lymphocytes, mainly due to the lack of analytical tools. However, the advent of third-generation sequencing technology, developed by Oxford Nanopore Technology, has now made it possible to map epitranscriptomics marks at the nucleotide level, although bioinformatic identification of such modifications remains challenging.

The main objectives of this project are to elucidate the roles of epitranscriptomic-associated enzymes in CD4+ T cells, notably by using sequencing of native RNA on Nanopore technology to map RNA modifications.