Alternative splicing modulation by G-quadruplexes

Alternative splicing is central to metazoan gene regulation but the regulatory mechanisms involved are only partially understood. Here, we show that G-quadruplex (G4) motifs are enriched ~3-fold both upstream and downstream of splice junctions. Analysis of in vitro G4-seq data corroborates their formation potential. G4s display the highest enrichment at weaker splice sites, which are frequently involved in alternative splicing events. The importance of G4s in RNA as supposed to DNA is emphasized by a higher enrichment for the non-template strand. To explore if G4s are involved in dynamic alternative splicing responses, we analyzed RNA-seq data from mouse and human neuronal cells treated with potassium chloride. We find that G4s are enriched at exons which were skipped following potassium ion treatment. We validate the formation of stable G4s for three candidate splice sites by circular dichroism spectroscopy, UV-melting and fluorescence measurements. Finally, we explore G4 motifs across eleven representative species, and we observe that strong enrichment at splice sites is restricted to mammals and birds.