Abstract
BackgroundAccurate mRNA splicing depends on multiple regulatory signals encoded in the transcribed RNA sequence. Many examples of mutations within human splice regulatory regions that alter splicing qualitatively or quantitatively have been reported and allelic differences in mRNA splicing are likely to be a common and important source of phenotypic diversity at the molecular level, in addition to their contribution to genetic disease susceptibility. However, because the effect of a mutation on the efficiency of mRNA splicing is often difficult to predict, many mutations that cause disease through an effect on splicing are likely to remain undiscovered.ResultsWe have combined a genome-wide scan for sequence polymorphisms likely to affect mRNA splicing with analysis of publicly available Expressed Sequence Tag (EST) and exon array data. The genome-wide scan uses published tools and identified 30,977 SNPs located within donor and acceptor splice sites, branch points and exonic splicing enhancer elements. For 1,185 candidate splicing polymorphisms the difference in splicing between alternative alleles was corroborated by publicly available exon array data from 166 lymphoblastoid cell lines. We developed a novel probabilistic method to infer allele-specific splicing from EST data. The method uses SNPs and alternative mRNA isoforms mapped to EST sequences and models both regulated alternative splicing as well as allele-specific splicing. We have also estimated heritability of splicing and report that a greater proportion of genes show evidence of splicing heritability than show heritability of overall gene expression level. Our results provide an extensive resource that can be used to assess the possible effect on splicing of human polymorphisms in putative splice-regulatory sites.ConclusionWe report a set of genes showing evidence of allele-specific splicing from an integrated analysis of genomic polymorphisms, EST data and exon array data, including several examples for which there is experimental evidence of polymorphisms affecting splicing in the literature. We also present a set of novel allele-specific splicing candidates and discuss the strengths and weaknesses of alternative technologies for inferring the effect of sequence variants on mRNA splicing.
Highlights
Accurate mRNA splicing depends on multiple regulatory signals encoded in the transcribed RNA sequence
We present a novel probabilistic method to infer allelic differences in mRNA splicing from Expressed Sequence Tag (EST) data, and use recently published Affymetrix exon array hybridisation data derived from 166 lymphoblastoid cell lines [25] for which genome-wide genotype data are available through the HapMap project [16] to test for association between mRNA isoforms and the genotype of putative cis-acting splicing polymorphisms
For each type of splice-regulatory element, publicly available tools were used to score the sequences associated with alternative Single Nucleotide Polymorphism (SNP) alleles and score differences for the identified polymorphisms are reported as supplementary data
Summary
Accurate mRNA splicing depends on multiple regulatory signals encoded in the transcribed RNA sequence. Many examples of mutations within human splice regulatory regions that alter splicing qualitatively or quantitatively have been reported and allelic differences in mRNA splicing are likely to be a common and important source of phenotypic diversity at the molecular level, in addition to their contribution to genetic disease susceptibility. The mechanisms through which genetic variants at many disease-associated loci affect disease susceptibility remain to be determined. Mutations or polymorphisms that affect mRNA splicing can have a profound effect on the function of the spliced product, but these effects are often difficult to predict from the primary genomic sequence. The medical and biological significance of such variants is evident from the large and rapidly increasing volume of literature reporting examples of aberrant mRNA splicing associated with human cancers and genetic diseases [2,3]. Point mutations leading to aberrant splicing are thought to be among the most important contributors to human genetic diseases [4]
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