A conserved RNA structure regulates polyamine‐dependent alternative splicing and NMD

Post‐transcriptional gene regulation in vertebrates can be mediated through coupling of alternative splicing to nonsense‐mediated decay (AS‐NMD), by controlling inclusion of stop codon‐containing exons (SCEs). Despite the absence of protein‐coding information, many SCEs are highly conserved, suggesting the presence of regulatory elements. We have identified a complex RNA structure spanning an SCE in a gene encoding a key enzyme in polyamine metabolism. In high levels of spermine or nonmetabolizable spermine analogs, the exon is skipped, increasing the levels of functional Spermine/Spermidine Acetyl Transferase (SSAT) mRNA. Depletion of spermine causes exon inclusion and decay of SSAT transcripts. We have shown that this structure is necessary and sufficient for the spermine‐regulated splicing. Detailed structure probing of a model RNA folded in the presence or absence of spermine shows that exon structure is profoundly influenced by spermine, but not spermidine, putrescene, ethylene diamine, or ammonium ion. The concentration of spermine required to change folding in vitro is between 10 and 50 uM, whereas intracellular concentrations of spermine are in the millimolar range. Once folded, the RNA structure is resistant to changes in spermine level. We suggest that splicing regulation of this SCE is mediated by the concentration of spermine (or another large polyamine in the cell), and that the exon senses this level directly. Control of alternative splicing by RNA structures for protein coding exons is rare in vertebrate genomes, however it may be more common in AS‐NMD, where the sequences of stop codon exons are free to evolve. Supported by NIH Grant GM040478.