The Basal State of Hox Gene Control and Function in Ray-finned Fish Phylogeny

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Hox genes encode transcriptional regulator proteins that play an important role in body axis formation and are likely to have a major influence on the development and evolution of body plans. Human and mouse possess thirty-nine Hox genes distributed on four Hox clusters, A, B, C, D. Recent studies have found a dynamic mode of Hox cluster evolution occurred in the ray-finned fishes. Derived ray-finned fishes (teleosts) such as zebrafish and pufferfish have 7-8 Hox clusters that have undergone considerable sequence evolution. Hence, comparisons of Hox gene control and function between taxa such as zebrafish and human are complicated. The PI will investigate Hox gene control and function in the bichir (Polypterus senegalus), the most basal living ray-finned fish that possesses several primitive fish morphological characters including primitive pectoral fins. The PI has already shown that the bichir has a single HoxA cluster; hence, the bichir does not have the duplication that produced extra HoxA clusters in derived teleosts. This research has three Objectives: (1) to determine the Hox complement of clusters and genes in the bichir, (2) to utilize bichir HoxA cluster sequences to identify HoxA11 cis-regulatory elements that are responsible for the expression pattern in an ancestral fish fin, and (3) to survey for the presence of so-identified ancestral HoxA11 cis-regulatory elements in additional teleost lineages. The experimental approach involves (1) cloning, sequencing, and informatics of bichir Hox clusters, (2) using transgenic reporter technologies to functionally test candidate ancestral HoxA11 cis-regulatory sequences, and (3) isolating HoxA clusters of additional teleost lineages with targeted sequencing of so-identified ancestral HoxA11 cis-regulatory sequences. Results of this research will contribute to a mechanistic foundation for the evolution of terrestrial limbs from aquatic fins. Knowledge on Hox gene control and function in the earliest ray-finned fishes will enhance understanding of the evolutionary forces acting on duplicated Hox clusters of derived ray-finned fishes. This research has/will generated a large body of genomic sequence data of Hox clusters in the bichir and other ray-finned fishes that are/will be deposited in GenBank and shared openly in the scientific community via research publications and websites. In terms of broader impact, this project will provide good training opportunities for undergraduate, graduate, and postdoctoral students in the postgenomic era.