» Articles » PMID: 29133793

Binding to SMN2 Pre-mRNA-protein Complex Elicits Specificity for Small Molecule Splicing Modifiers

Abstract

Small molecule splicing modifiers have been previously described that target the general splicing machinery and thus have low specificity for individual genes. Several potent molecules correcting the splicing deficit of the SMN2 (survival of motor neuron 2) gene have been identified and these molecules are moving towards a potential therapy for spinal muscular atrophy (SMA). Here by using a combination of RNA splicing, transcription, and protein chemistry techniques, we show that these molecules directly bind to two distinct sites of the SMN2 pre-mRNA, thereby stabilizing a yet unidentified ribonucleoprotein (RNP) complex that is critical to the specificity of these small molecules for SMN2 over other genes. In addition to the therapeutic potential of these molecules for treatment of SMA, our work has wide-ranging implications in understanding how small molecules can interact with specific quaternary RNA structures.

Citing Articles

RNA-binding proteins as therapeutic targets in cancer.

Jungfleisch J, Gebauer F RNA Biol. 2025; 22(1):1-8.

PMID: 40016176 PMC: 11869776. DOI: 10.1080/15476286.2025.2470511.


Three- and four-stranded nucleic acid structures and their ligands.

Hashimoto Y, Shil S, Tsuruta M, Kawauchi K, Miyoshi D RSC Chem Biol. 2025; .

PMID: 40007865 PMC: 11848209. DOI: 10.1039/d4cb00287c.


Patient-specific responses to splice-modifying treatments in spinal muscular atrophy fibroblasts.

Signoria I, Zwartkruis M, Geerlofs L, Perenthaler E, Faller K, James R Mol Ther Methods Clin Dev. 2024; 32(4):101379.

PMID: 39655308 PMC: 11626024. DOI: 10.1016/j.omtm.2024.101379.


A sequential binding mechanism for 5' splice site recognition and modulation for the human U1 snRNP.

White D, Dunyak B, Vaillancourt F, Hoskins A Nat Commun. 2024; 15(1):8776.

PMID: 39389991 PMC: 11467380. DOI: 10.1038/s41467-024-53124-5.


: an integrative toolkit for splicing analysis from short-read RNA-seq.

Rot G, Wehling A, Schmucki R, Berntenis N, Zhang J, Ebeling M Bioinform Adv. 2024; 4(1):vbae121.

PMID: 39219843 PMC: 11364168. DOI: 10.1093/bioadv/vbae121.


References
1.
Singh N, Lee B, Singh R . Splicing regulation in spinal muscular atrophy by an RNA structure formed by long-distance interactions. Ann N Y Acad Sci. 2015; 1341:176-87. PMC: 4651915. DOI: 10.1111/nyas.12727. View

2.
Roca X, Akerman M, Gaus H, Berdeja A, Bennett C, Krainer A . Widespread recognition of 5' splice sites by noncanonical base-pairing to U1 snRNA involving bulged nucleotides. Genes Dev. 2012; 26(10):1098-109. PMC: 3360564. DOI: 10.1101/gad.190173.112. View

3.
Fu X . The superfamily of arginine/serine-rich splicing factors. RNA. 1995; 1(7):663-80. PMC: 1369309. View

4.
Kotake Y, Sagane K, Owa T, Mimori-Kiyosue Y, Shimizu H, Uesugi M . Splicing factor SF3b as a target of the antitumor natural product pladienolide. Nat Chem Biol. 2007; 3(9):570-5. DOI: 10.1038/nchembio.2007.16. View

5.
Singh N, Androphy E, Singh R . An extended inhibitory context causes skipping of exon 7 of SMN2 in spinal muscular atrophy. Biochem Biophys Res Commun. 2004; 315(2):381-8. DOI: 10.1016/j.bbrc.2004.01.067. View