Cloning of a Novel Homeobox-Containing Gene,PKNOX1,and Mapping to Human Chromosome 21q22.3

Abstract

To contribute to the development of the transcript map of human chromosome 21 and to the understanding of the pathogenesis of Down syndrome, we have used exon trapping to identify portions of genes from pools of HC21-specific cosmids. More than 550 potential exons have been isolated to date. One such trapped exon, hmc37a09 (GenBank Accession No. X88106), was identical to a region of a human EST, L12425 (GenBank Accession No. D31072). Its predicted amino acid sequence was homologous to the homeodomain region of homeobox-containing genes. Using the trapped sequence and the EST as probes to screen human fetal brain and kidney cDNA libraries, we have cloned the corresponding full-length cDNA. This novel gene encodes a homeodomain-containing polypeptide of 436 amino acids. The most closely related sequence is that of the mouseMeis1,aPBX-like homeobox gene. The homeodomain of the novel gene is closely related to those of the mammalianPBXfamily and the plantKnotted1family (involved in plant development). This gene is namedPKNOX1by the Human Nomenclature Committee. By PCR amplification, hybridization, and genetic linkage analysis using a (GT)npolymorphism in the 3′UTR, we have precisely localizedPKNOX1to chromosome 21q22.3 between markers D21S212 and D21S25 on YAC350F7.PKNOX1is expressed in many human tissues tested by Northern blot analysis. The involvement of thePKNOX1gene in Down syndrome and/or monogenic disorders associated with dysfunction of this gene is presently unknown. Targeted disruption of thePKNOX1homolog in mice will enhance our understanding of its biological function in normal mammalian development.