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Human Molecular Genetics, 1999, Vol. 8, No. 7 1177-1183
© 1999 Oxford University Press

Article

A single nucleotide difference that alters splicing patterns distinguishes the SMA gene SMN1 from the copy gene SMN2

Umrao R. Monani1, Christian L. Lorson4, D. William Parsons2, Thomas W. Prior2, Elliot J. Androphy4,5, Arthur H. M. Burghes1,3,a and John D. McPherson6

Departments of 1Neurology, 2Pathology and 3Medical Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Departments of 4Dermatology and 5Molecular Biology and Microbiology, New England Medical Center and Tufts University School of Medicine, Boston, MA 02111, USA and 6Genome Sequencing Center/Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA

Spinal muscular atrophy (SMA) is a recessive disorder characterized by loss of motor neurons in the spinal cord. It is caused by mutations in the telomeric survival motor neuron 1 (SMN1) gene. Alterations within an almost identical copy gene, the centromeric survival motor neuron 2 (SMN2) gene produce no known phenotypic effect. The exons of the two genes differ by just two nucleotides, neither of which alters the encoded amino acids. At the genomic level, only five nucleotides that differentiate the two genes from one another have been reported. The entire genomic sequence of the two genes has not been determined. Thus, differences which might explain why SMN1 is the SMA gene are not readily apparent. In this study, we have completely sequenced and compared genomic clones containing the SMN genes. The two genes show striking similarity, with the homology being unprecedented between two different yet functional genes. The only critical difference in an ~32 kb region between the two SMN genes is the C->T base change 6 bp inside exon 7. This alteration but not other variations in the SMN genes affects the splicing pattern of the genes. The majority of the transcript from the SMN1 locus is full length, whereas the majority of the transcript produced by the SMN2 locus lacks exon 7. We suggest that the exon 7 nucleotide change affects the activity of an exon splice enhancer. In SMA patients, the loss of SMN1 but the presence of SMN2 results in low levels of full-length SMN transcript and therefore low SMN protein levels which causes SMA.

a To whom correspondence should be addressed at: Department of Medical Biochemistry, 363 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210, USA. Tel: +1 614 688 4710; Fax: +1 614 292 4118; Email: burghes.1{at}osu.edu

DDBJ/EMBL/GenBank accession nos AC004999 and AC005031.


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S. Jablonka, B. Schrank, M. Kralewski, W. Rossoll, and M. Sendtner
Reduced survival motor neuron (Smn) gene dose in mice leads to motor neuron degeneration: an animal model for spinal muscular atrophy type III
Hum. Mol. Genet., February 12, 2000; 9(3): 341 - 346.
[Abstract] [Full Text] [PDF]

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 Hum Mol GenetHome page
C. L. Lorson and E. J. Androphy
An exonic enhancer is required for inclusion of an essential exon in the SMA-determining gene SMN
Hum. Mol. Genet., January 22, 2000; 9(2): 259 - 265.
[Abstract] [Full Text] [PDF]

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 J. Biol. Chem.Home page
S. R. Lim and K. J. Hertel
Modulation of Survival Motor Neuron Pre-mRNA Splicing by Inhibition of Alternative 3' Splice Site Pairing
J. Biol. Chem., November 21, 2001; 276(48): 45476 - 45483.
[Abstract] [Full Text] [PDF]

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 J. Biol. Chem.Home page
P. J. Young, P. M. Day, J. Zhou, E. J. Androphy, G. E. Morris, and C. L. Lorson
A Direct Interaction between the Survival Motor Neuron Protein and p53 and Its Relationship to Spinal Muscular Atrophy
J. Biol. Chem., January 18, 2002; 277(4): 2852 - 2859.
[Abstract] [Full Text] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
Y. Hofmann, C. L. Lorson, S. Stamm, E. J. Androphy, and B. Wirth
Htra2-beta 1 stimulates an exonic splicing enhancer and can restore full-length SMN expression to survival motor neuron 2 (SMN2)
PNAS, August 15, 2000; 97(17): 9618 - 9623.
[Abstract] [Full Text] [PDF]


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