Schematic illustrating the methods for genotyping and detecting allele-specific expression. (A) Routine gene-expression analysis using mRNA. Signals from all probes interrogating the same ORF are averaged to produce an estimate of the gene-expression level. In this example, the probe signals suggest that the reference strain (red) expresses this ORF at a higher level than the test strain (blue). All probes hybridize equally well in the test strain, providing no evidence of sequence mismatches between the probe and target sequence. (B) Genotyping using genomic DNA. When DNA is hybridized to arrays, the intensities in the two strains are the same, except at probes interrogating sequences where the test strain bears a polymorphism. Here, the test strain bears a polymorphism in the region interrogated by “Probe 4,” and as a result, the test strain produces a weak signal at this probe. (C) Genotyping using mRNA. The gene is expressed at a different level in the test strain than in the reference strain, but the polymorphism in the sequence interrogated by “Probe 4” is still readily detected, because the signal at this probe is substantially less than the gene-expression level as estimated using the entire probe set. (D) Equal expression of both alleles in a diploid. A diploid strain formed by mating the reference and test strains (green) is heterozygous for the sequence polymorphism at “Probe 4.” The ratio of the intensity at “Probe 4” to the remaining probes in the heterozygous diploid is equal to the average of the ratios of “Probe 4” to the remaining probes in the reference and test strains, suggesting that both alleles are expressed in equal amounts. (E) Preferential expression of the reference strain allele. Here, the ratio of the intensity at “Probe 4” to the remaining probe is the same as the ratio in the reference strain, suggesting that only the allele derived from the reference strain is expressed. (F) Preferential expression of the test strain allele.
