Abstract
BackgroundAllele-specific expression (ASE) assays can be used to identify cis, trans, and cis-by-trans 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.ResultsWe 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.ConclusionWe 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.
Highlights
Allele-specific expression (ASE) assays can be used to identify cis, trans, and cis-bytrans regulatory variation
Digital ASE assay In this study, we introduce an accurate approach to allelespecific expression assays that relies on read counts generated from Solexa sequencing
When we planned on analyzing more than one sample per gene, a unique forward primer was ordered for each sample that contained the common elements described above, plus a unique one to three base pair barcode sequence in the 5' tail that will allow for individual sample identification (Figure 1a)
Summary
Allele-specific expression (ASE) assays can be used to identify cis, trans, and cis-bytrans regulatory variation. Understanding the source of expression variation has important implications for disease susceptibility, phenotypic diversity, and adaptation. 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 [1,2,3], and more specific aims such as deciphering how genetic variation in humans may affect response to treatment [4,5]. By partitioning regulatory variation into cis, trans, and cis-by-trans, we can identify their respective contributions to changes in gene expression (page number not for citation purposes)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
