RNA-Seq and Chem-CLIP-Seq analysis of a r(CUG)exp degrader in DM1
In brief, a panel of RNA focused low molecular weight fragments containing a photosensitive diazirine and alkyne tag was screened by an in vitro target-based assay and allowing for the identification of a compound that binds r(CUG)exp. Indeed, this simple novel small molecule has been discovered to selectively engage r(CUG) repeats in vitro through various biophysical methods as well as in DM1 patient-derived myotubes harboring a long and toxic r(CUG)exp in the DMPK mRNA. Selectivity and target engagement was further evaluated transcriptome-wide by associating Chem-CLIP (chemical crosslinking and isolation by pulldown) and RNA sequencing (RNA-seq) which confirmed binding to DMPK amongst other RNA targets. Lastly, this molecule was converted into a site-specific RNA cleaver using bleomycin, which displayed broad rescue of the DM1-associated defects by RNA-seq. This is a supplemental dataset for our manuscript describing more in details about our method.