Allele-specific expression assays using Solexa

Abstract

<p>Abstract</p> <p>Background</p> <p>Allele-specific expression (ASE) assays can be used to identify <it>cis</it>, <it>trans</it>, and <it>cis</it>-by-<it>trans </it>regulatory variation. Understanding the source of expression variation has important implications for disease susceptibility, phenotypic diversity, and adaptation. While ASE is commonly measured via relative fluorescence at a SNP, next generation sequencing provides an opportunity to measure ASE in an accurate and high-throughput manner using read counts.</p> <p>Results</p> <p>We introduce a Solexa-based method to perform large numbers of ASE assays using only a single lane of a Solexa flowcell. In brief, transcripts of interest, which contain a known SNP, are PCR enriched and barcoded to enable multiplexing. Then high-throughput sequencing is used to estimate allele-specific expression using sequencing counts. To validate this method, we measured the allelic bias in a dilution series and found high correlations between measured and expected values (r>0.9, p < 0.001). We applied this method to a set of 5 genes in a <it>Drosophila simulans </it>parental mix, F1 and introgression and found that for these genes the majority of expression divergence can be explained by <it>cis</it>-regulatory variation.</p> <p>Conclusion</p> <p>We present a new method with the capacity to measure ASE for large numbers of assays using as little as one lane of a Solexa flowcell. This will be a valuable technique for molecular and population genetic studies, as well as for verification of genome-wide data sets.</p