Allele-specific expression assays using Solexa

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 Drosophila simulans parental mix, F1 and introgression and found that for these genes the majority of expression divergence can be explained by cis-regulatory variation.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.Genotype-phenotype mapping is a fundamental aim of biological science. This is critical for many goals such as understanding of how genetic architecture shapes phenotypic variation and adaptation [1-3], and more specific aims such as deciphering how genetic variation in humans may affect response to treatment [4,5]. Many genetic variants resulting in phenotypic differences are mediated through changes in gene expression. Thus, analyzing gene expression allows us to better understand genotypic variation. Variation in gene expression can be due to polymorphisms both at the gene locus (cis) and in other genes that influence its expression (trans), as well as the non-additive interactions between the two (cis-by-trans) [6]. Furthermore, epigenetic mechanisms [7], chromatin conformation [8], copy number variation [9,10] and microRNA [11] all play important roles in the transcription of a given gene. By partitioning regulatory variation into cis, trans, and cis-by-trans, we can identify their respective c