Highlights

The basic layout of the vertebrate body is outlined in the axial progenitors mostly through Hox-independent mechanisms.

Hox genes are carriers of patterning information loaded onto the derivatives of axial progenitors that guides the production of body structures congruent with their axial level.

Selective target inactivation allows the shutting down of a subset of Hox-dependent functions while keeping others active in the same domain. This increases the flexibility of evolutionary processes.

The processes regulating Hox gene expression in the proximal and distal regions of the limb buds occur in two alternative functional chromatin domains.

Modification of Hox regulatory processes within chromatin domains might have played a role in the evolution of vertebrate paired appendages.