title: Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations: a synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer.
abstract: The idea that point mutations in exons may affect splicing is intriguing and adds an additional layer of complexity when evaluating their possible effects. Even in the best-studied examples, the molecular mechanisms are not fully understood. Here, we use patient cells, model minigenes, and in vitro assays to show that a missense mutation in exon 5 of the medium-chain acyl-CoA dehydrogenase (MCAD) gene primarily causes exon skipping by inactivating a crucial exonic splicing enhancer (ESE), thus leading to loss of a functional protein and to MCAD deficiency. This ESE functions by antagonizing a juxtaposed exonic splicing silencer (ESS) and is necessary to define a suboptimal 3' splice site. Remarkably, a synonymous polymorphic variation in MCAD exon 5 inactivates the ESS, and, although this has no effect on splicing by itself, it makes splicing immune to deleterious mutations in the ESE. Furthermore, the region of MCAD exon 5 that harbors these elements is nearly identical to the exon 7 region of the survival of motor neuron (SMN) genes that contains the deleterious silent mutation in SMN2, indicating a very similar and finely tuned interplay between regulatory elements in these two genes. Our findings illustrate a mechanism for dramatic context-dependent effects of single-nucleotide polymorphisms on gene-expression regulation and show that it is essential that potential deleterious effects of mutations on splicing be evaluated in the context of the relevant haplotype.
authors.affiliation: Research Unit for Molecular Medicine, Aarhus University Hospital and Faculty of Health Science, Skejby Sygehus, Denmark.
authors.forename: Karsten Bork
authors.initials: KB
authors.lastname: Nielsen
authors.forename: Suzette
authors.initials: S
authors.lastname: Sørensen
authors.forename: Luca
authors.initials: L
authors.lastname: Cartegni
authors.forename: Thomas Juhl
authors.initials: TJ
authors.lastname: Corydon
authors.forename: Thomas Koed
authors.initials: TK
authors.lastname: Doktor
authors.forename: Lisbeth Dahl
authors.initials: LD
authors.lastname: Schroeder
authors.forename: Line Sinnathamby
authors.initials: LS
authors.lastname: Reinert
authors.forename: Orly
authors.initials: O
authors.lastname: Elpeleg
authors.forename: Adrian R
authors.initials: AR
authors.lastname: Krainer
authors.forename: Niels
authors.initials: N
authors.lastname: Gregersen
authors.forename: Jørgen
authors.initials: J
authors.lastname: Kjems
authors.forename: Brage Storstein
authors.initials: BS
authors.lastname: Andresen
mesh_terms: D042964:Acyl-CoA Dehydrogenase / Q000235:genetics*; D017362:Cyclic AMP Response Element-Binding Protein / Q000235:genetics / Q000378:metabolism; D017931:DNA Primers / Q000235:genetics; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D005091:Exons / Q000235:genetics*; D005260:Female; D019398:Genes, BRCA1 / Q000502:physiology; D006801:Humans; D007109:Immunity; D007223:Infant; D007231:Infant, Newborn; D008052:Lipid Metabolism, Inborn Errors / Q000235:genetics / Q000276:immunology*; D008969:Molecular Sequence Data; D009134:Muscular Atrophy, Spinal / Q000235:genetics / Q000276:immunology; D020125:Mutation, Missense / Q000235:genetics; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D012326:RNA Splicing / Q000235:genetics*; D020871:RNA Stability / Q000235:genetics; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D055532:SMN Complex Proteins; D012689:Sequence Homology, Nucleic Acid; D037941:Silencer Elements, Transcriptional / Q000235:genetics*; D055540:Survival of Motor Neuron 2 Protein; D014158:Transcription, Genetic
chemical_list: D017362:Cyclic AMP Response Element-Binding Protein; D017931:DNA Primers; D009419:Nerve Tissue Proteins; D016601:RNA-Binding Proteins; D055532:SMN Complex Proteins; C526477:SMN2 protein, human; D055540:Survival of Motor Neuron 2 Protein; D042964:Acyl-CoA Dehydrogenase