A position-dependent organisation of retinoid response elements is conserved in the vertebrate Hox clusters

Unlike the genetic code, the protein-DNA recognition modalities are degenerate in both directions. Consequently, how do transcription factors achieve their considerable specificity and selectivity in regulating the genetic programs that they ultimately influence? Here, we discuss the fact that different Hox gene-specific variants of retinoid response elements are not equivalent. Each particular variant occurs at a precise position along the vertebrate Hox clusters and this organization was present before the time when the ancestral vertebrate Hox cluster was duplicated.