G-quadruplexe as a structural modulator of Intron Retention upon viral infection

Amongst the wide array of alternative splicing events (ASE), the intrinsic mechanisms of intron retention have remained elusive. This particular type of ASE has long been characterized as an artifact, but recent studies have shown its implication in numerous diseases. It has also been revealed that numerous viruses choose to disrupt alternative splicing to escape cellular immune response and further their proliferation. The main focus of this study was to investigate the G-quadruplex role in Alternative Splicing Events (ASEs) that occur following Flavivirus infections. After having demonstrated that G-quadruplexes structures are mainly formed in Intron Retained Transcripts by RNA-seq, our attention turned toward the ULK3 gene, coding for a serine/threonine kinase regulating autophagy, an essential mechanism in the cellular response to stress and even pathogen infections. In this study, we revealed the presence of a G-quadruplex in the first intron of the ULK3 gene near the 3 splice site. Furthermore, we assayed the formation and stability of this G-quadruplex in vitro and showed that its formation affects IR, as demonstrated by comparisons between wild-type and mutant transfected mini-genes. Finally, we identified the specific RNA-binding protein signature for this G-quadruplex, thereby uncovering the novel role of G-quadruplexes in Alternative Splicing.