et al. 1995; Chambon 1996). For example, a functional inverted repeat with zero nucleotides in the spacer (IR0) was recently described (Lee and Wei 1999). A large number of genes containing RAREs have now been identified, and the transcription of many has been shown to be modulated by RA treatment (Chambon 1996; Collins and Mao 1999). Similarly, the expression of numerous genes has been observed to change following embryonic RA exposure. How many of these changes are directly controlled by RAREs and which are critical for teratogenicity is largely unknown. The HOX genes, however, represent one class of functionally important downstream RA targets in teratogenesis.

The homeobox-containing HOX transcription factors are involved in patterning of the CNS, limbs, axial skeleton, and other organ systems, where their expression encodes positional identity. As discussed in Chapter 6, HOX genes are arranged on chromosomes in clusters in which the genes are colinear with their expression domains (Duboule 1998). For example, in the early CNS and somites, 3′ HOX genes are expressed rostrally and 5′ caudally. This colinearity is also manifest in responsiveness to RA, the induction of 3′ HOX genes being more rapid and abundant (Marshall et al. 1996). Endogenous retinoid signaling might be responsible for the progressive expression of HOX genes in vivo. The primitive (Hensen’s) node, for example, is a site of RA synthesis and might pattern the paraxial mesoderm as it egresses through the primitive streak (Hogan et al. 1992). Exogenous retinoids can induce ectopic, expanded, or reduced HOX expression domains, which then establish abnormally arranged compartments of positional identity. These abnormal compartments then result in abnormal cell fate and morphogeneisis (Marshall et al. 1996).

There is good evidence for HOX-mediated retinoid teratogenicity in the axial skeleton, craniofacies, and limb, but perhaps the best understood example is the developmental effect in the hindbrain. The different HOX genes encode transcription factors that control the different identities of the rhombomeres (r) of the hindbrain. Hoxb2 has a rostral expression boundary at r2-3, Hoxb3 at r4-5, Hoxb4 at r6-7, and Hoxb1 in a band at r4 (Marshall et al. 1996; Studer et al. 1996). At early neural-plate stages in the mouse, exogenous retinoid treatment results in rostral expansion of these domains. In some cases, the treatment results in a transformation of r1-3 to an r4 identity with expansion of r5 (Conlon and Rossant 1992). In other cases, r2-3 is transformed into r4-5, and both the trigeminal motor nucleus and adjacent trigeminal ganglion are transformed into structures having a facial nucleus or ganglion appearance (Marshall et al. 1992). Analyses of the 3′ Hox genes reveal multiple RAREs that cooperate with other positive and negative regulatory elements to regulate spatial and temporal expression of the HOX genes (Marshall et al. 1996).

Retinoid-induced changes in HOX gene expression probably result in abnormally arranged compartments of HOX expression. The misexpressed HOX gene then activates and represses many other genes in abnormal places and thereby initiates abnormal development. Pathogenetic changes observed in retinoid-

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