Determinants of Exon 7 Splicing in the Spinal Muscular Atrophy Genes, SMN1 and SMN2

• Published in: American journal of human genetics 2006-01, Vol.78 (1), p.63-77
• Main Authors: Cartegni, Luca, Hastings, Michelle L., Calarco, John A., de Stanchina, Elisa, Krainer, Adrian R.
• Format: Article
• Language: English
• Subjects: Base Sequence; Binding sites; Biological and medical sciences; Cyclic AMP Response Element-Binding Protein - genetics; Cyclic AMP Response Element-Binding Protein - metabolism; Degenerative and inherited degenerative diseases of the nervous system. Leukodystrophies. Prion diseases; Diseases of striated muscles. Neuromuscular diseases; Exons - genetics; Gene Expression; General aspects. Genetic counseling; Heterogeneous-Nuclear Ribonucleoprotein Group A-B - metabolism; Humans; Medical genetics; Medical sciences; Models, Genetic; Molecular Sequence Data; Muscular Atrophy, Spinal - genetics; Muscular system; Mutagenesis; Mutation; Mutation - genetics; Nerve Tissue Proteins - genetics; Nerve Tissue Proteins - metabolism; Neurological disorders; Neurology; Nuclear Proteins - metabolism; Oligonucleotides; Promoter Regions, Genetic - genetics; RNA Interference; RNA Splicing - genetics; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Serine-Arginine Splicing Factors; SMN Complex Proteins; Survival of Motor Neuron 1 Protein; Survival of Motor Neuron 2 Protein
• ISSN: 0002-9297; 1537-6605
• DOI: 10.1086/498853

Spinal muscular atrophy is a neurodegenerative disorder caused by the deletion or mutation of the survival-of-motor-neuron gene, SMN1. An SMN1 paralog, SMN2, differs by a C→T transition in exon 7 that causes substantial skipping of this exon, such that SMN2 expresses only low levels of functional protein. A better understanding of SMN splicing mechanisms should facilitate the development of drugs that increase survival motor neuron (SMN) protein levels by improving SMN2 exon 7 inclusion. In addition, exonic mutations that cause defective splicing give rise to many genetic diseases, and the SMN1/2 system is a useful paradigm for understanding exon-identity determinants and alternative-splicing mechanisms. Skipping of SMN2 exon 7 was previously attributed either to the loss of an SF2/ASF–dependent exonic splicing enhancer or to the creation of an hnRNP A/B–dependent exonic splicing silencer, as a result of the C→T transition. We report the extensive testing of the enhancer-loss and silencer-gain models by mutagenesis, RNA interference, overexpression, RNA splicing, and RNA-protein interaction experiments. Our results support the enhancer-loss model but also demonstrate that hnRNP A/B proteins antagonize SF2/ASF–dependent ESE activity and promote exon 7 skipping by a mechanism that is independent of the C→T transition and is, therefore, common to both SMN1 and SMN2. Our findings explain the basis of defective SMN2 splicing, illustrate the fine balance between positive and negative determinants of exon identity and alternative splicing, and underscore the importance of antagonistic splicing factors and exonic elements in a disease context.