Collaborative Research: Resolving the gene regulatory network alterations responsible for the repeated evolution of a Hox-regulated trait

生物外观（或“表型”）的一个统一特征是它在发育过程中的构造。每个表型性状都需要一组基因的合作，这些基因的参与是由被称为顺式调控元件（CREs）的DNA序列控制的。cre就像开关一样，在特定的生命阶段，打开或关闭某些细胞类型的基因。cre的开关功能是通过被称为转录因子的蛋白质特异性结合的有序碱基的短片段在DNA序列中编码的。转录因子的组合形成了一个指令的“逻辑”，它精确地决定了哪些细胞，以及在什么时候CRE可以开启一个基因。目前，人们对开关类功能如何在cre中编码以及特征如何通过编码逻辑的变化而进化仍然知之甚少。特别是，Hox转录因子代表了一个鲜为人知的类别，它为cre提供了沿主体轴的位置信息。Williams和Rebeiz的实验室正在合作研究果蝇（Drosophila melanogaster）雄性特异性身体色素的基因网络和cre。结果将告诉我们这种色素沉着是如何在果蝇的多个谱系中起源和改变的。这些结果将显示Hox基因、cre如何控制新特征的构建，以及进化如何在转录因子结合位点水平上起作用。这项工作将提供一个特征进化的图片，将适用于各种各样的动物系统。通过这项研究，计算工具将得到改进，在线学习资源将被创建，以帮助科学家。该研究项目将通过高中生、本科生和研究生参与指导研究来支持未来的科学人才。参与将强调来自科学领域代表性不足群体的学生。塑造动物身体计划的发育事件被认为是新性状进化的一个坩埚。该项目的总体目标是了解身体计划模式信息如何起源于基因调控网络（GRN），并随后被修改以使形态特征多样化。grn的结构是通过转录因子与顺式调控元件（CREs）的结合来控制基因表达。结合CREs的因素组合形成一个调控逻辑，指定时间、模式和表达水平。目前，关于GRN结构如何进化产生不同表型的了解甚少。具体来说，层次结构中的哪些基因被修改了，以及最终调控逻辑是如何进化的。Williams和Rebeiz的实验室正在研究GRN的进化及其潜在的调控逻辑，这是一种在实验中易于处理的动物系统中出现的快速进化特征。拟议的研究将集中在雄性腹部色素沉着模式上，这种模式在两个果蝇谱系中趋同进化，然后被修改并丢失。第一个目标将描述身体计划的仲裁人（例如Hox蛋白、辅助因子和活性调节剂）如何直接与GRN的cre相互作用，以控制黑腹虾色素沉着酶的表达模式。第二个目标将确定在非模式果蝇物种中，当色素沉着扩大、收缩或丢失时，这种由hox调节的GRN是如何改变的。第三个目标将追踪该GRN如何在非模型苍蝇中独立进化出收敛色素沉着表型。为了实现这些目标，研究小组将采用技术，包括在多种果蝇物种中进行报告基因转基因，以及在转录因子和CRE序列之间进行凝胶转移测定，以查明表型改变突变，并将这些突变与转录因子结合和功能的改变联系起来。

A unifying feature of an organism's appearance (or "phenotype") is its construction during the events of development. Each phenotypic trait requires the cooperation of a collection of genes whose participation is controlled by DNA sequences known as cis-regulatory elements (CREs). CREs work like switches to turn genes ON or OFF in certain cell types at specific life stages. The switch-like function of CREs are encoded in the DNA sequence by short stretches of ordered bases to which proteins known as transcription factors specifically bind. Combinations of transcription factors form a "logic" of instructions that determines precisely which cells, and at what time the CRE can switch a gene ON. Currently, it remains poorly understood how switch-like functions are encoded in CREs and how traits evolve through changes in their encoded logic. In particular, the Hox transcription factors represent a poorly understood class that provides CREs with positional information along the major body axis. The Williams and Rebeiz labs are collaborating to study the network of genes and CREs responsible for making a male-specific body pigmentation of the fruit fly species Drosophila melanogaster. The results will inform how such pigmentation originated and was altered in multiple lineages of fruit fly species. The outcomes will show how the construction of a new characteristic is controlled by Hox genes, CREs and how evolution can operate at the level of binding sites for transcription factors. This work will provide a picture of trait evolution that will be applicable to a wide variety of animal systems. Through this research, computational tools will be refined and online learning resources will be created to aid scientists. This research project will support the future of science personnel through the participation of high school students, undergraduate students, and graduate students in mentored research. Participation will emphasize students from under-represented groups in science.The developmental events that pattern the animal body plan are regarded as a crucible for the evolution of novel traits. This project's overarching goal is to understand how body plan patterning information originated in a gene regulatory network (GRN), and was subsequently modified to diversify a morphological trait. GRNs are structured to pattern development through the binding of transcription factors to cis-regulatory elements (CREs) to control gene expression. The combination of factors that bind CREs form a regulatory logic that specifies timing, pattern and levels of expression. Currently, very little is known about how GRN structure evolves to generate different phenotypes. Specifically, which genes in the hierarchy were modified, and ultimately how regulatory logic evolves. The Williams and Rebeiz labs are examining the evolution of a GRN and its underlying regulatory logic for a rapidly evolving trait present in an experimentally tractable animal system. The proposed studies will focus on male-specific patterns of abdominal pigmentation that convergently evolved in two fruit fly lineages, which were then modified and lost. The first aim will characterize how the arbiters of the body plan (e.g. Hox proteins, cofactors, and activity modulators) directly interact with CREs of the GRN to control expression patterns of pigmentation enzymes in D. melanogaster. The second aim will determine how this Hox-regulated GRN was altered in cases where pigmentation was expanded, contracted, or lost in non-model fruit fly species. The third aim will trace how this GRN independently evolved a convergent pigmentation phenotype in a non-model fly. To pursue these aims, the research team will employ techniques that include reporter transgenes in multiple fruit fly species and gel shift assays between transcription factors and CRE sequences to pinpoint phenotype altering mutations and connect these to the alterations in transcription factor binding and function that they inspired.