Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1


Alteration of correct splicing patterns by disruption of an exonic splicing enhancer may be a frequent mechanism by which point mutations cause genetic diseases. Spinal muscular atrophy results from the lack of functional survival of motor neuron 1 gene (SMN1), even though all affected individuals carry a nearly identical, normal SMN2 gene. SMN2 is only partially active because a translationally silent, single-nucleotide difference in exon 7 causes exon skipping. Using ESE motif-prediction tools, mutational analysis and in vivo and in vitro splicing assays, we show that this single-nucleotide change occurs within a heptamer motif of an exonic splicing enhancer, which in SMN1 is recognized directly by SF2/ASF. The abrogation of the SF2/ASF-dependent ESE is the basis for inefficient inclusion of exon 7 in SMN2, resulting in the spinal muscular atrophy phenotype.

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Figure 1: High-score SR protein motifs in exon 7 of SMN1 and SMN2.
Figure 2: Effect of point mutations on calculated SC35 and SF2/ASF motif scores.
Figure 3: Exon 7–skipping correlates with disruption of the proximal SF2/ASF heptamer motif.
Figure 4: The SMN1 SF2/ASF heptamer motif is a bona fide ESE.
Figure 5: SF2/ASF promotes inclusion of SMN1 exon 7 in vitro.
Figure 6: SF2/ASF binds directly to the high-score motif in SMN1 exon 7.
Figure 7: Model of SF2/ASF-dependent exon 7 inclusion in SMN1 and SMN2.


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We thank M. Hastings and J. Zhu for sharing reagents and for helpful comments on the manuscript. We are grateful to C. Lorson and E. Androphy for the pCITel plasmid and for helpful discussions. This work was supported by the National Institutes of Health (National Institute of General Medical Sciences and National Institute of Neurological Disorders and Stroke), by Andrew's Buddies Corp., and by a postdoctoral fellowship from the Human Frontiers Science Program (to L.C.).

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Correspondence to Adrian R. Krainer.

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Cartegni, L., Krainer, A. Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nat Genet 30, 377–384 (2002). https://doi.org/10.1038/ng854

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