Homeobox-containing genes have been implicated in a variety of patterning events during vertebrate limb development. In an attempt to isolate cDNAs corresponding to 5' members of the chicken HOX 4 cluster of homeobox-containing genes, a cDNA library constructed from mRNAs expressed during early stages of chick limb development was screened with probes generated by the polymerase chain reaction (PCR) using oligonucleotide primers corresponding to sequences in the homeoboxes of the human HOX4C and HOX4F genes, the human homologs of Hox-4.4 and Hox-4.6. This screening resulted in the isolation of full length cDNAs for the chicken homolog of HOX4F (cognate of mouse Hox-4.6), which we have termed GHox-4.6, and the chicken homolog of human HOX1I, which we have named GHox-1i, a paralog of Hox-4.6 in the HOX 1 cluster. The homeodomains encoded by GHox-4.6 and GHox-1i differ by only three amino acids, and the two proteins show extensive similarity along their entire lengths. Despite their sequence similarity, in situ hybridization analysis has revealed that GHox-4.6 and GHox-1i exhibit strikingly different spatial patterns of expression during embryonic chick limb development. At early stages of limb development (stages 20-22), GHox-4.6 transcripts are present in high amounts throughout the posterior half of the limb mesoderm and are absent from the anterior half of the mesoderm, an expression pattern consistent with the possible involvement of GHox-4.6 in the specification of posterior positional identity. In contrast, GHox-1i exhibits no distinct anterior-posterior polarity of expression at stage 22, but rather is expressed in high amounts throughout the mesenchyme of the limb bud. At later stages of development (stage 25), GHox-1i continues to be expressed in high amounts throughout the undifferentiated mesenchyme subjacent to the apical ectodermal ridge, and, in addition, is expressed in the mesodermal cells in the proximal peripheral regions of the limb bud subjacent to the ectoderm which are differentiating into nonchondrogenic lineages. Conversely, little or no expression of GHox-1i is detectable in the proximal central core of the limb bud where chondrogenic differentiation is occurring. Thus, GHox-1i is expressed by the undifferentiated subridge mesenchymal cells and proximal peripheral mesenchymal cells of the limb bud that are being inhibited from undergoing chondrogenesis by the apical ectodermal ridge and nonridge ectoderm.(ABSTRACT TRUNCATED AT 400 WORDS)