A Toxic RNA Catalyzes the Cellular Synthesis of Its Own Inhibitor, Shunting It to Endogenous Decay Pathways

SUMMARY Myotonic dystrophy type 2 (DM2) is a genetically defined muscular dystrophy caused by a toxic expanded repeat of r(CCUG) [heretofore (CCUG) exp ], harbored in intron 1 of CHC-Type Zinc Finger Nucleic Acid Binding Protein ( CNBP ) pre-mRNA. This r(CCUG) exp causes DM2 via a gain-of-function mechanism that results in three hallmarks of its pathology: (i) binding to RNA-binding proteins (RBPs) that aggregate into nuclear foci; (ii) sequestration of muscleblind-like-1 (MBNL1) protein, a regulator of alternative pre-mRNA splicing, leading to splicing defects; and (iii) retention of intron 1 in the CNBP mRNA. Here, we find that CNBP intron retention is caused by the r(CCUG) exp -MBNL1 complex and can be rescued by small molecules. We studied two types of small molecules with different modes of action, ones that simply bind and ones that can be synthesized by a r(CCUG) exp -templated reaction in cells, that is the RNA synthesizes its own drug. Indeed, our studies completed in DM2 patient-derived fibroblasts show that the compounds disrupt the r(CCUG) exp -MBNL1 complex, reduce intron retention, subjecting the liberated intronic r(CCUG) exp to native decay pathways, and rescue other DM2-associated cellular defects. Collectively, this study shows that small molecules can affect RNA biology by shunting toxic transcripts towards native decay pathways. HIGHLIGHTS Intron retention in RNA repeat expansions can be due to repeats binding to proteins Small molecules that bind RNA repeats and inhibit protein binding can trigger decay A toxic RNA repeat can catalyze the synthesis of its own inhibitor on-site On-site drug synthesis most potently affects disease biology eTOC BLURB The most common way to target RNA is to use antisense oligonucleotides to target unstructured RNAs for destruction. Here, we show for the first time that small molecules targeting structured, disease-causing RNAs can shunt them towards native decay pathways by affecting their processing.