Alu insertion variants alter mRNA splicing.

Lindsay M Payer,Peter A Calabresi,Janiece Walker,Thomas A Cooper,Kathryn C Fitzgerald,Jared P Steranka,Daniel Ardeljan,Kathleen H Burns

doi:10.1093/nar/gky1086

Abstract

RNA splicing is a highly regulated process dependent on sequences near splice sites. Insertions of Alu retrotransposons can disrupt splice sites or bind splicing regulators. We hypothesized that some common inherited polymorphic Alu insertions are responsible for splicing QTLs (sQTL). We focused on intronic Alu variants mapping within 100 bp of an alternatively used exon and screened for those that alter splicing. We identify five loci, 21.7% of those assayed, where the polymorphic Alu alters splicing. While in most cases the Alu promotes exon skipping, at one locus the Alu increases exon inclusion. Of particular interest is an Alu polymorphism in the CD58 gene. Reduced CD58 expression is associated with risk for developing multiple sclerosis. We show that the Alu insertion promotes skipping of CD58 exon 3 and results in a frameshifted transcript, indicating that the Alu may be the causative variant for increased MS risk at this locus. Using RT-PCR analysis at the endogenous locus, we confirm that the Alu variant is a sQTL for CD58. In summary, altered splicing efficiency is a common functional consequence of Alu polymorphisms including at least one instance where the variant is implicated in disease risk. This work broadens our understanding of splicing regulatory sequences around exons.

Highlights

Alternative splicing of transcripts is pervasive in the genome, with >95% of genes generating more than one mRNA by alternative splicing [1]
Most sequence determinants of splicing occur proximal to exon boundaries (e.g. [28,29]), and we expected that the Alu elements altering splicing would most likely fall within the previously reported ‘underrepresentation zone’ that spans 100 bp 5 and 3 of exons [21]
To test the hypothesis that Alu polymorphisms alter mRNA splicing resulting in an effect on gene function and disease risk, we evaluated two instances where an Alu variant near an alternatively spliced exon occurred in proximity to a genome-wide association study (GWAS) signal [22]

Summary

Introduction

Alternative splicing of transcripts is pervasive in the genome, with >95% of genes generating more than one mRNA by alternative splicing [1]. When splicing is skewed beyond normal alternative splicing, the aberrant resultant isoform can result in a disease phenotype In between these two extremes, it is possible that common variants subtly alter mRNA splicing with modest phenotypic outcomes, such as increasing common disease risk [7]. We investigated whether commonly occurring polymorphic Alu elements can alter splicing and affect mRNA isoform prevalence. These structural variants exist in the population with both the Alu-containing allele and the pre-insertion (no Alu) allele present These structural variants exist in the population with both the Alu-containing allele and the pre-insertion (no Alu) allele present (e.g. [8])

Methods

Results

Conclusion