De novo mutations affecting the pre-mRNA
splicing
factor U2AF2 are associated with developmental delays and intellectual
disabilities, yet the molecular basis is unknown. Here, we demonstrated
by fluorescence anisotropy RNA binding assays that recurrent missense
mutants (Arg149Trp, Arg150His, or Arg150Cys) decreased the binding
affinity of U2AF2 for a consensus splice site RNA. Crystal structures
at 1.4 Å resolutions showed that Arg149Trp or Arg150His disrupted
hydrogen bonds between U2AF2 and the terminal nucleotides of the RNA
site. Reanalysis of publicly available RNaseq data confirmed that
U2AF2 depletion altered splicing of transcripts encoding RNA binding
proteins (RBPs). These results confirmed that the impaired RNA interactions
of Arg149Trp and Arg150His U2AF2 variants could contribute to dysregulating
an RBP-governed neurodevelopmental program of alternative splicing.