Homeotic genes regulate the coordinated activity of other genes involved in the development of body regions.  In the fruit fly Drosophila melanogaster, genes controlled by  homeotic regions called "homeoboxs" act on one or more regions in the body of mature Drosophila larvae called "imaginal discs," controlling normal body structure development.
The Antennapedia (Antp) complex, found on thoracic segment 2 (T2), regulates the development of legs where the antenna are normally found.  When a probe made with the Antp gene was hybridized with fly genomic DNA, it was found to bind not only to its own sequence, but also to the fushi tarazu (ftz) region, which is involved with the regulation of body segment development.  This and other homeobox sequences show remarkable homology (75-90%) with Drosophila, human, yeast mating-type (MAT) genes, and the operator and repressor segments of prokaryotic operons.


Using in situ hybridization (insertion of radioactive probes in tissue DNA) it is possible to examine homeotic gene expression directly.  Such studies show that more than one homeotic protein can be localized per cell during development, and that several of these are likely to compete for binding to promoter sequences.  This is demonstrated by the competition between the Antennapedia complex (ANT-C) at T2 and Ultrabithorax locus (Ubx), a subdivision of the bithorax region of  T3.  When Ubx is removed, Antp proteins bind to regulatory regions normally controlled by Ubx proteins, resulting in the antennapedia mutation.

It is likely that homeotic genes regulate cascades of biosynthesis leading to the expression of tissue-specific proteins.  Thus, a mutation in a single homeotic gene could result in major alterations in the body plan of an organism during development.