SF3B1 Phosphorylation Prompts U2AF2 Dissociation for Widespread Control of Pre-mRNA Splicing

SF3B1, a core spliceosome subunit, is extensively phosphorylated before the first catalytic step of pre-mRNA splicing. Intriguingly, most SF3B1 phosphorylation sites surround its binding sites for U2AF2, an early-stage pre-mRNA splicing factor.

Here, we discovered that SF3B1 phosphorylation significantly decreases its association with U2AF2. We determined three crystal structures revealing electrostatic repulsion between an acidic U2AF2 alpha helix and the negatively charged phosphoryl group of SF3B1. Variants with amino acid substitutions that prevent or mimic SF3B1 phosphorylation perturbed thousands of splice sites, primarily those marked by uridine-rich splice site signals recognized by U2AF2.