Figure 3.

Description of the F₀/F₁ ASE test for cis- and trans-acting gene expression regulation. (A) Each inbred parent possesses only the cis and trans factors associated with that genotype, while the F₁ hybrid possesses both. (B) In the simplest case where ASE patterns are affected by a single cis element, allelic imbalance ratios are identical across generations. (C) In the case where a single trans factor causes ASE variation, the F₁ ASE counts should be identical for both alleles since both trans factors are acting on each allele. To illustrate the effects of cis- and trans-by-treatment interactions, take the case where an experimental treatment induces the expression of a HAL2-specific cis- or trans-acting repressor (green symbol, dashed lines). The resultant expression patterns would shift so that the difference between alleles (cis-by-treatment, D) or the slope of the genotype*generation interaction depends on the treatment (trans-by-treatment, E). The scheme presented here is a simplification, and all combinations of cis, trans additive effects and interactions with the environment are possible.