Figure 4. Allele-specific expression (ASE) assays demonstrate cis-regulatory changes in Pitx1 and Tbx5.
(A) Schematic of ASE assay using Tbx5 expression as an example. Differences in Tbx5 expression between scale-footed and feather-footed breeds could be due to trans- and/or cis-acting mutations. If expression differences between parental breeds are due to trans changes only (stars), then expression of the two Tbx5 alleles in hybrid embryos will be the same (top right). In contrast, if cis-regulatory changes underlie differences in Tbx5 expression between the parental breeds, then expression of the two Tbx5 alleles in hybrid embryos will be different (bottom right). (B-D) ASE assay in hybrid hindlimb buds indicate cis-regulatory divergence between scale-footed (Old Dutch Capuchine) and muffed (fairy swallow) pigeon breeds in Pitx1 (B) and Tbx5 (C), but not in Tbx3 (D). Dashed blue line indicates null hypothesis of equal expression of alleles. (E) ASE assay in hybrid hindlimb buds indicate cis-regulatory divergence in Tbx5 between feather-footed (silkie) and scale-footed (white leghorn) chicken breeds. Boxes in (B-E) span 1st to 3rd quartiles, bars extend to minimum and maximum observed values if within 1.5 times the interquartile range of the box, circles indicate values outside of this range, black line indicates median. **p≤0.01 ***p≤0.005.
DOI: http://dx.doi.org/10.7554/eLife.12115.016