title: Identification of common genetic variation that modulates alternative splicing.
abstract: Alternative splicing of genes is an efficient means of generating variation in protein function. Several disease states have been associated with rare genetic variants that affect splicing patterns. Conversely, splicing efficiency of some genes is known to vary between individuals without apparent ill effects. What is not clear is whether commonly observed phenotypic variation in splicing patterns, and hence potential variation in protein function, is to a significant extent determined by naturally occurring DNA sequence variation and in particular by single nucleotide polymorphisms (SNPs). In this study, we surveyed the splicing patterns of 250 exons in 22 individuals who had been previously genotyped by the International HapMap Project. We identified 70 simple cassette exon alternative splicing events in our experimental system; for six of these, we detected consistent differences in splicing pattern between individuals, with a highly significant association between splice phenotype and neighbouring SNPs. Remarkably, for five out of six of these events, the strongest correlation was found with the SNP closest to the intron-exon boundary, although the distance between these SNPs and the intron-exon boundary ranged from 2 bp to greater than 1,000 bp. Two of these SNPs were further investigated using a minigene splicing system, and in each case the SNPs were found to exert cis-acting effects on exon splicing efficiency in vitro. The functional consequences of these SNPs could not be predicted using bioinformatic algorithms. Our findings suggest that phenotypic variation in splicing patterns is determined by the presence of SNPs within flanking introns or exons. Effects on splicing may represent an important mechanism by which SNPs influence gene function.
authors.affiliation: University Department of Paediatrics, John Radcliffe Hospital, Oxford, United Kingdom. jeremy.hull@paediatrics.ox.ac.uk
authors.forename: Jeremy
authors.initials: J
authors.lastname: Hull
authors.forename: Susana
authors.initials: S
authors.lastname: Campino
authors.forename: Kate
authors.initials: K
authors.lastname: Rowlands
authors.forename: Man-Suen
authors.initials: MS
authors.lastname: Chan
authors.forename: Richard R
authors.initials: RR
authors.lastname: Copley
authors.forename: Martin S
authors.initials: MS
authors.lastname: Taylor
authors.forename: Kirk
authors.initials: K
authors.lastname: Rockett
authors.forename: Gareth
authors.initials: G
authors.lastname: Elvidge
authors.forename: Brendan
authors.initials: B
authors.lastname: Keating
authors.forename: Julian
authors.initials: J
authors.lastname: Knight
authors.forename: Dominic
authors.initials: D
authors.lastname: Kwiatkowski
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D002460:Cell Line; D005091:Exons / Q000235:genetics; D014644:Genetic Variation; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000502:physiology*; D020033:Protein Isoforms / Q000235:genetics* / Q000502:physiology; D022821:RNA Splice Sites / Q000235:genetics
chemical_list: D020033:Protein Isoforms; D022821:RNA Splice Sites