All-Atom Simulations Elucidate the Impact of U2AF2 Cancer- Associated Mutations on Pre-mRNA Recognition

The U2AF2 splicing factor, made of two tandem RNA recognition motifs (RRMs) joined by a flexible linker, selects the intronic polypyrimidine sequence of premature mRNA, thus ensuring splicing fidelity. Increasing evidence links mutations of key splicing factors, including U2AF2, to a variety of cancers. Nevertheless, the impact of U2AF2 cancer-associated mutations on polypyrimidine recognition remains unclear. Here, we combined extensive (18 mu s-long) all-atom molecular dynamics simulations and dynamical network theory analysis (NWA) of U2AF2, in its wild-type form and in the presence of the six most frequent cancer associated mutations, bound to a poly-U strand. Our results reveal that the selected mutations affect the pre-mRNA binding at two hot spot regions, irrespectively of where these mutants are placed on the distinct U2AF2 domains. Complementarily, NWA traced the existence of cross-communication pathways, connecting each mutation site to these recognition hot spots, whose strength is altered by the mutations. Our outcomes suggest the existence of a structural/dynamical interplay of the two U2AF2's RRMs underlying the recognition of the polypyrimidine tract and reveal that the cancer-associated mutations affect the polypyrimidine selection by altering the RRMs' cooperativity. This mechanism may be shared by other RNA binding proteins hallmarked, like U2AF2, by multidomain architecture and high plasticity.

Automated summary

In this study, we investigated the impact of U2AF2 cancer-associated mutations on polypyrimidine recognition through extensive molecular dynamics simulations and dynamical network analysis. Our results showed that these mutations affect the binding of U2AF2 to the polypyrimidine sequence, regardless of their location on the distinct domains of U2AF2. We also identified cross-communication pathways between the mutation sites and recognition hot spots, whose strength is altered by the mutations. These findings suggest a structural/dynamical interplay of U2AF2 domains underlying polypyrimidine recognition and reveal the impact of cancer-associated mutations on the cooperativity of U2AF2 domains in polypyrimidine selection.