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

Abstract

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 approximately 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.

Baseline results of the NeuroNEXT spinal muscular atrophy infant biomarker study

“…SMA is caused by homozygous deletion or mutation in the SMN1 ( survival motor neuron 1 ) gene and retention of the nearly identical gene, SMN2 ( survival motor neuron 2 ), which results in reduced expression of full‐length SMN protein 3, 4. In humans, SMN2 is present in the same genomic region and differs from SMN1 by a single‐nucleotide substitution that results in the exclusion of exon 7 in approximately 90% of SMN transcripts 5, 6. The mRNA that results, SMNΔ7, produces a truncated protein that is nonfunctional and targeted for degradation 7, 8…”

Treatment of spinal muscular atrophy cells with drugs that upregulate SMN expression reveals inter- and intra-patient variability

“…The SMN2 gene, however, contains a T nucleotide at this position, leading to a differentially spliced form that lacks exon 7 (D7-SMN). 2,[6][7][8] The resulting putative shorter protein has a different C-terminus. It is less stable and cannot oligomerize or self-associate, as occurs with the complete protein.…”

An in vivo reporter system for measuring increased inclusion of exon 7 in SMN2 mRNA: potential therapy of SMA

“…It is estimated that more than 80% of SMN2 transcripts exclude exon 7. 16,19 Lorson et al 16 have recently reported that a single nucleotide difference at the sixth nucleotide position in exon 7 (7+6 position) is responsible for the alternative splicing. When the nucleotide is 'C' as in SMN1, exon 7 is recognized and included.…”