Structural analysis of chemically probed pre-mRNA structure using RADIS

Yet experimentally grounded structural models for human pre-mRNAs have been largely restricted to experimentally grounded structural models for human pre-mRNAs have been largely restricted to splice-site-proximal regions, leaving the deep intronic regions, where ~70% of intronic disease-causing variants reside, almost entirely unmapped.

We developed RADIS (Reactivity Analysis of Deep and Intergenic RNA Structure), a strategy that yields strand-resolved chemical probing reactivity profiles across entire intron-rich loci by creating tiled arrays of RNAs that comprehensively span long genomic distances. This approach removes the abundance and locus-specificity constraints that otherwise limit pre-mRNA probing approaches. RADIS recovers known E. coli ribosomal RNA architectures and yields high-correlation in-cell dimethyl sulfate (DMS)-MaP reactivities at representative splice sites (r = 0.87–0.90).