Hox genes coordinate the formation of the branchial region of vertebrate embryos, which involves neural crest cells, visceral arches, and the developing brain. Hox gene expression pattering also allows for cranial patterning in the rhombomeres. There are a number of Hox genes, which are selectively expressed in cells based on their initial location in the fetus. (Hall, 32)

For example, Hox-3 genes play a role in the development of the thymus and thyroid, and pattern neuroectoderm and mesenchyme from the neural crest. Neural crest cells migrating from the hindbrain express a combination of Hox genes depending upon their initial locus in the brain.

Polycomb response elements within the regulatory regions of the homeotic genes are important regulators of Hox genes in vertebrates. Disruption of the polycomb elements causes skeletal transformations and defective neural crest derivatives: the eye, cleft palate, ectopic occipital bones, abnormal parathyroids, and thymus and heart defects. (Hall, 167)