m6A RNA methylation: a new pathway controlling endogenous retroviruses – MARMER

Endogenous retroviruses (ERVs) form a large and heterogenous group of retrotransposons that sum up 10% of the mouse and human genomes. Over the course of evolution, ERVs acted as an important and beneficial source of genetic innovations. However, on the short term, ERVs can compromise genomic integrity through their retrotransposition or their mere presence. In mice, 12% of spontaneous pathological mutations result from de novo ERV insertions, half of which originate from a single family of the ERVK class, the Intracisternal A particles (IAP). In contrast, human ERVs are mostly immobile. However, independently of their mobilization, ERVs can divert regulatory networks and cellular states by providing promoters and enhancers. Moreover, ERVs generate RNA, cDNA, RNA:DNA hybrid species and proteins, the accumulation of which is associated and may contribute to senescence, cancer and neurodegenerative diseases. To restrain their deleterious effects, ERVs are controlled at each step of their RNA-centered life cycle. In particular, chromatin-based silencing by DNA methylation and histone modifications and post-transcriptional control through RNA editing and RNA interference have been extensively characterized. However, these control mechanisms are not active in all cell types or developmental periods, suggesting that other ERV limiting pathways have yet to be uncovered.

Using a genome-scale loss-of-function screen, we have recently discovered that the N6-methyladenosine (m6A) modification controls ERV mRNAs in mouse embryonic stem cells. The m6A modification is known as a critical determinant of mRNA fate—including export, decay and translation—in an array of biological processes such as embryonic development, cell proliferation and differentiation, genomic integrity maintenance and stress responses. Accordingly, this pathway has been linked to many pathologies, including autoimmune diseases, neurodegenerative disorders and cancer. However, while these processes have been related to functions that m6A exert on genic mRNAs, they have not been considered yet with the prism of ERV biology.

Capitalizing on the expertise of two scientific partners in the fields of transposable elements and RNA biology, the MARMER program aims at determining: 1) the spectrum of action of m6A methylation on the metabolism of ERV mRNAs; 2) the evolutionary conservation of this new ERV restricting pathway in humans, and 3) the RNA binding proteins that mediate the fate of m6A -methylated ERV mRNAs. The basis of this work will employ inducible and reversible systems to modulate m6A levels in cells, ultra-long read direct sequencing of m6A RNA modification and complementary assays to analyze transcription, shuffling, decay and translation of ERV mRNAs. It also relies on an innovative technology for the identification of m6A-dependent RNA-protein interactions and further validation of their functional relevance. By connecting m6A RNA modification and ERV regulation, the scope of our proposal is entirely novel and tantalizingly, will add another mean by which the m6A RNA modification is essential for cellular identity and genomic stability. The mechanistic and functional insights we will provide are an absolute prerequisite for investigating the function of m6A -dependent ERV regulation in development and disease.