Project B13 – Dissecting the regulatory mechanisms of alternative polyadenylation and nuclear retention of mRNAs by SR proteins

The aim of this project is to investigate how SR proteins connect pre-mRNA splicing with alternative polyadenylation (APA) and the nuclear export or retention of specific mRNA isoforms. In the previous funding period, we started with a comprehensive analysis of the entire SR protein family (SRSF1-SRSF7) to differentiate their specific functions. We discovered that SRSF3 and SRSF7 are the major players that regulate APA in opposing directions and connect it to mRNA export. This changes the mRNA’s fate from being productively exported and translated in the cytoplasm to being retained in the nucleus. Mechanistically, we found that SRSF7 and SRSF3 compete for binding to proximal poly(A) sites (pPAS) and promote or inhibit their usage. In parallel, we reported that SRSF5 effects a switch from export to retention of its target mRNAs during neuronal differentiation through a reversible inhibition of its nucleo-cytoplasmic shuttling capacities. In the next funding period, we wish to pursue how these three SR proteins control APA and nuclear retention and to investigate the consequences of impaired regulation for the cells. We aim to dissect the molecular mechanisms of how SRSF3 and SRSF7 antagonistically regulate pPAS usage, including the role of m6A modifications and the identification of RNA elements and RBPs that co-regulate PAS choice. In a second aim, we will investigate the factors that control the switch in nuclear retention of SRSF5 mRNPs during neuronal differentiation and probe the role of nuclear bodies in this process.