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A negative element in SMN2 exon 7 inhibits splicing in spinal muscular atrophy

Nature Genetics volume 34, pages 460–463 (2003)Cite this article

Abstract

Spinal muscular atrophy (SMA) is a relatively common neurodegenerative disease caused by homozygous loss of the survival motor neuron 1 (SMN1) gene1. Humans possess a linked, nearly identical gene, SMN2, which produces a functional SMN protein but at levels insufficient to compensate for loss of SMN1 (refs. 1,2). A C/T transition at position +6 in exon 7 is all that differentiates the two genes, but this is sufficient to prevent efficient exon 7 splicing in SMN2 (refs. 2,3). Here we show that the C/T transition functions not to disrupt an exonic splicing enhancer (ESE) in SMN1 (ref. 4), as previously suggested, but rather to create an exonic splicing silencer (ESS) in SMN2. We show that this ESS functions as a binding site for a known repressor protein, hnRNP A1, which binds to SMN2 but not SMN1 exon 7 RNA. We establish the physiological importance of these results by using small interfering RNAs to reduce hnRNP A protein levels in living cells and show that this results in efficient SMN2 exon 7 splicing. Our findings not only define a new mechanism underlying the inefficient splicing of SMN2 exon 7 but also illustrate more generally the remarkable sensitivity and precision that characterizes control of mRNA splicing.

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Figure 1: ASF/SF2 does not have an essential role in SMN exon 7 splicing.
Figure 2: The C→U transition in SMN2 creates a sequence with properties of an hnRNP A1–dependent ESS.
Figure 3: In vivo depletion of hnRNP A1 or A2 proteins by RNA interference restores SMN2 exon 7 inclusion.
Figure 4: Model for regulation of exon 7 splicing in SMN1 and SMN2 precursor mRNAs.

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Acknowledgements

We thank Y. Takebayashi for technical assistance, C.L. Lorson for advice on cloning SMN1 and SMN2 minigene constructs, R. Tacke for providing human Tra2α and Tra2β cDNAs, H.J. Okano for mouse HuD cDNA, J. Kohtz for antibodies to ASF/SF2 and I. Boluk for help preparing the manuscript. This work was supported by grants from the US National Institutes of Health and Families of SMA.

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  1. Department of Biological Sciences, Columbia University, New York, 10027, New York, USA

    Tsuyoshi Kashima & James L Manley

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Correspondence to James L Manley.

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Kashima, T., Manley, J. A negative element in SMN2 exon 7 inhibits splicing in spinal muscular atrophy. Nat Genet 34, 460–463 (2003). https://doi.org/10.1038/ng1207

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