Polyamine-dependent metabolic shielding regulates alternative splicing

Metabolites are central to cellular homeostasis. Whereas much emphasis has been placed on their relevance to meet energetic and biosynthetic demands, metabolic intermediates also function as signaling molecules. Here we show that polyamines, small polycations critical to cellular homeostasis1-3, regulate the process of alternative pre-mRNA splicing. We find that the inhibition of polyamine synthesis increases the phosphorylation of spliceosomal proteins, concomitant with a remarkable perturbation of alternative splicing in cells and tissues. Mechanistically, molecular modeling combined with biochemical assays revealed that polyamines bind to acidic phosphorylatable motifs in splicing factors of the U2 snRNP SF3 subcomplex, thus preventing the action of kinases. The molecular process through which polyamines regulate protein phosphorylation is a phenomenon that we define as “metabolic shielding”. Overall design: Deep-coverage RNA-seq analysis to test the effect of polyamine biosynthesis inhibition on splicing in DU145 cells. Deep-coverage RNA-seq analysis to test the effect of polyamine biosynthesis inhibition on splicing upon the absence or presence of U2 snRNP SF3A3 subcomplex member. Deep-coverage RNA-seq analysis to test the effect of polyamine biosynthesis inhibition on splicing in the skeletal muscle of wild-type mice. Deep-coverage RNA-seq analysis to test the effect of polyamine biosynthesis inhibition on splicing in HeLa cells. Deep-coverage RNA-seq analysis to test the effect of polyamine biosynthesis inhibition on splicing in mouse embryonic stem cells under the effect of SAM486A and DFMO Deep-coverage RNA-seq analysis to test the effect of polyamine biosynthesis inhibition on splicing in mouse embryonic stem cells under the effect of SAM486A, DFMO and BENSpm