The expression of zebrafish hoxb3a and hoxb4a has been found to be mediated 
through five transcripts, hoxb3a transcripts I-III and hoxb4a transcripts I-II, 
driven by four promoters. A "master" promoter, located about 2 kb downstream of 
hoxb5a, controls transcription of a pre-mRNA comprising exon sequences of both 
genes. This unique gene structure is proposed to provide a novel mechanism to 
ensure overlapping, tissue-specific expression of both genes in the posterior 
hindbrain and spinal cord. Transgenic approaches were used to analyze the 
functions of zebrafish hoxb3a/hoxb4a promoters and enhancer sequences containing 
regions of homology that were previously identified by comparative genomics. Two 
neural enhancers were shown to establish specific anterior expression borders 
within the hindbrain and mediate expression in defined neuronal populations 
derived from hindbrain rhombomeres (r) 5 to 8, suggesting a late role of the 
genes in neuronal cell lineage specification. Species comparison showed that the 
zebrafish hoxb3a r5 and r6 enhancer corresponded to a sequence within the mouse 
HoxA cluster controlling activity of Hoxa3 in r5 and r6, whereas a homologous 
region within the HoxB cluster activated Hoxb3 expression but limited to r5. We 
conclude that the similarity of hoxb3a/Hoxa3 regulatory mechanisms reflect the 
shared descent of both genes from a single ancestral paralog group 3 gene.