Alignment of HOXC5, C6 and C8 Genes on Chicken Chromosome 1: Dispersion of a Vertebrate HOX Cluster?

Abstract

Hox genes are known to be master regulators of body plan in multicellular organisms. Within vertebrates, Hox genes are typically arranged into tight clusters (confined to ~0.1 Mb) on separate chromosomes, perhaps conserved as clusters through shared cis-regulatory regions. There are four Hox clusters (A, B, C, and D) in land vertebrates. In chicken (Gallus gallus), HOX clusters have been tentatively assigned with HOXAs linked to chr 2, HOXBs to chr 3, HOXDs to chr 7, and HOXCs to chr 1. However, the precise locations of many of these associated genes have yet to be described. Using cDNA sequences of HOXC5, C6, and C8, we conducted BLAST queries of the available Gallus gallus genome. Exonic and 3′UTR sequences of HOXC6 mapped to ~102.5 Mb on chr 1. While the HOXC8 gene mapped to ~87.9 Mb, thus separating these “contiguous” genes by about 14.6 Mb. Sequences from the 5′UTR of HOXC5 were found ~0.5 Mb into a supercontig yet to be linked chromosomally. As more detailed genomic maps become available, it seems likely that this supercontig associated with HOXC5 will be located downstream of HOXC6 on chromosome 1, which would then separate these genes by at least ~1.7 Mb. Furthermore, although the HOXBs are assigned to chr 3, HOXB8 aligns to chr 27. Within a vertebrate it is surprising to find HOX genes widely dispersed, and possibly even on separate chromosomes as with HOXB8. If the genomic map is correct, then the chicken HOXB and C clusters may be cases of dispersed vertebrate Hox clusters like those reported in some invertebrates. This would have significant implications for the role of shared cis-regulatory regions on the evolutionary and functional conservation of Hox gene clustering.