DIVERGENT GENE EXPRESSION OF HOXB3B IN TELEOST FISHES IS DUE TO DIVERGENCE OF UPSTREAM CIS-REGULATORY ELEMENTS
Hox genes are developmental regulatory genes that function to pattern the cranial nerves that are derived from the rhombomeres (r) during vertebrate embryonic development. Hoxb3, in particular, has been shown to be expressed in r5-7 in several tetrapod species, including mouse (Mus musculus). Over the course of evolution, teleost fish have undergone a whole genome duplication, and several species have retained both duplicate Hoxb3 genes, hoxb3a and hoxb3b. These genes are expressed differently from each other, such that while hoxb3a is expressed in r4- 7 in many teleost fish species, hoxb3b is expressed solely in r4. The cis-regulatory elements (CREs) that are responsible for directing hoxb3b expression in r4 are currently unknown. We used several software programs, including VISTA and CLUSTAL, to identify conserved sequences upstream of hoxb3b in the Japanese medaka (Oryzias latipes), Nile tilapia (Oreochromis niloticus), Atlantic salmon (Salmo salar), and Japanese pufferfish (Takifugu rubripes). From these analyses, we observed the presence of several CREs that are similar in sequence to those that direct other Hox genes in r4, including Hoxb1, Hoxa2, and Hoxb2. We also used these software programs to understand if the conserved sequences upstream of hoxb3b were present for hoxb3a in the same teleosts mentioned above, as well as hoxb3a in zebrafish (Danio rerio), Hoxb3 in the spotted gar, a species of bony fish that predates the teleost-specific genome duplication, and Hoxb3 of the dogfish shark (Scyliorhinus canicula), coelacanth (Latimeria chalumnae), mouse, and human (Homo sapiens). Interestingly, we did not observe the presence of the teleost hoxb3b-specific sequences for any Hoxb3 or hoxb3a gene. These results suggest that the whole genome duplication in teleost fishes has allowed for the divergence in expression and function of hoxb3b.