Gene

Splice site mutation

Cell biology

Biology

Enhancer

Small molecule

Intron

Structural biology

Small nuclear RNA

Computational biology

Spliceosome

Exonic splicing enhancer

Genetics

Splicing factor

Nucleic acid structure

RNA splicing

Non-coding RNA

Alternative splicing

Chemistry

Exon

Gene expression

snRNP

Nature Chemical Biology

Splicing modifiers promoting SMN2 exon 7 inclusion have the potential to treat spinal muscular atrophy, the leading genetic cause of infantile death. These small molecules are SMN2 exon 7 selective and act during the early stages of spliceosome assembly. Here, we show at atomic resolution how the drug selectively promotes the recognition of the weak 5ʹ splice site of SMN2 exon 7 by U1 snRNP. The solution structure of the RNA duplex formed following 5ʹ splice site recognition in the presence of the splicing modifier revealed that the drug specifically stabilizes a bulged adenine at this exon–intron junction and converts the weak 5ʹ splice site of SMN2 exon 7 into a stronger one. The small molecule acts as a specific splicing enhancer cooperatively with the splicing regulatory network. Our investigations uncovered a novel concept for gene-specific alternative splicing correction that we coined 5ʹ splice site bulge repair. NMR-based structural analysis of the RNA duplex formed by SMN2 exon 7 and U1 snRNA reveals that the splicing modifier SMN-C5 pulls the bulged adenine into the RNA helix base stack and transforms the weak 5ʹ splice site of SMN2 exon 7 into a stronger one.

Structural basis of a small molecule targeting RNA for a specific splicing correction