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

HOX基因编码转录调节蛋白，在体轴的形成中发挥重要作用，并可能对身体计划的发展和进化产生重大影响。人类和小鼠都有39个HOX基因，分布在A、B、C、D四个HOX簇上。最近的研究发现，在鳍鱼中出现了一种HOX簇进化的动态模式。衍生的鳍鱼(硬骨鱼)，如斑马鱼和河豚，有7-8个HOX簇，经历了相当大的序列进化。因此，斑马鱼和人类等类群之间的HOX基因控制和功能的比较是复杂的。PI将研究Hox基因在Bichir(Polypterus Senegalus)中的控制和功能，Bichir(Polypterus Senegalus)是最基本的活射线鳍鱼类，具有几种原始的鱼类形态特征，包括原始的胸鳍。PI已经表明，Bichir只有一个HoxA簇；因此，Bichir没有在衍生硬骨鱼中产生额外HoxA簇的复制。这项研究有三个目标：(1)确定Bichir中簇和基因的Hox互补；(2)利用Bichir HoxA簇序列来识别决定祖先鱼鳍表达模式的HoxA11顺式调控元件；以及(3)调查在其他硬骨鱼谱系中是否存在如此确定的祖先HoxA11顺式调控元件。实验方法包括(1)Bichir HOX簇的克隆、测序和信息学，(2)使用转基因报告技术对候选的祖先HoxA11顺式调控序列进行功能测试，以及(3)通过对如此确定的祖先HoxA11顺式调控序列的定向测序来分离额外的硬骨血统的HoxA簇。这项研究的结果将有助于从水生鳍进化成陆生肢体的机制基础。对最早的鳍鱼的HOX基因控制和功能的了解将加强对作用于衍生鳍鱼的重复HOX簇的进化力量的理解。这项研究已经/将产生大量Bichir和其他鳍鱼中Hox簇的基因组序列数据，这些数据将保存在GenBank中，并通过研究出版物和网站在科学界公开分享。在更广泛的影响方面，该项目将为后基因组时代的本科生、研究生和博士后提供良好的培训机会。

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.