Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure

Nucleic Acids Res. 2013 Apr 1;41(6):3819-32. doi: 10.1093/nar/gkt063. Epub 2013 Feb 7.


The serotonin receptor 2C plays a central role in mood and appetite control. It undergoes pre-mRNA editing as well as alternative splicing. The RNA editing suggests that the pre-mRNA forms a stable secondary structure in vivo. To identify substances that promote alternative exons inclusion, we set up a high-throughput screen and identified pyrvinium pamoate as a drug-promoting exon inclusion without editing. Circular dichroism spectroscopy indicates that pyrvinium pamoate binds directly to the pre-mRNA and changes its structure. SHAPE (selective 2'-hydroxyl acylation analysed by primer extension) assays show that part of the regulated 5'-splice site forms intramolecular base pairs that are removed by this structural change, which likely allows splice site recognition and exon inclusion. Genome-wide analyses show that pyrvinium pamoate regulates >300 alternative exons that form secondary structures enriched in A-U base pairs. Our data demonstrate that alternative splicing of structured pre-mRNAs can be regulated by small molecules that directly bind to the RNA, which is reminiscent to an RNA riboswitch.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing / drug effects*
  • Base Sequence
  • Exons
  • HEK293 Cells
  • High-Throughput Screening Assays
  • Humans
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Phylogeny
  • Pyrvinium Compounds / metabolism
  • Pyrvinium Compounds / pharmacology*
  • RNA Editing
  • RNA Precursors / metabolism
  • RNA, Double-Stranded / chemistry
  • RNA, Double-Stranded / drug effects
  • RNA, Messenger / chemistry
  • RNA, Messenger / drug effects*
  • RNA, Messenger / metabolism
  • Receptor, Serotonin, 5-HT2C / genetics*
  • Receptor, Serotonin, 5-HT2C / metabolism
  • Ribonucleoprotein, U1 Small Nuclear / metabolism
  • Spliceosomes / metabolism


  • Pyrvinium Compounds
  • RNA Precursors
  • RNA, Double-Stranded
  • RNA, Messenger
  • Receptor, Serotonin, 5-HT2C
  • Ribonucleoprotein, U1 Small Nuclear
  • pyrvinium