Rough genes with Deformed homeobox substitutions exhibit rough regulatory specificity during Drosophila eye development.

In certain cases, homeobox genes with different in vivo roles encode proteins with similar in vitro DNA binding specificities. To test the role of the homeobox in the regulatory specificity of such genes, rough homeobox sequences were changed in part or entirely to those of the Deformed gene, and the modified rough genes tested for their ability to rescue the rough mutant phenotype. Surprisingly, the chimaeric genes retained levels of rough regulatory specificity but acquired no novel functions. These results suggest that factors other than the DNA binding specificity of the homeodomain play crucial roles in determining the target, and thus the regulatory specificity, of such proteins.