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

生物体外观(或“表型”)的一个统一特征是它在发育过程中的结构。每个表型性状都需要一组基因的合作，这些基因的参与由被称为顺式调控元件(Cres)的DNA序列控制。CRE的工作原理就像开关一样，在特定的生命阶段打开或关闭特定细胞类型的基因。在DNA序列中，Cres的开关样功能是由一小段有序碱基编码的，被称为转录因子的蛋白质特定地结合在这些碱基上。转录因子的组合形成了一个指令的“逻辑”，它准确地决定了Cre可以打开哪些细胞，以及何时可以打开基因。目前，人们仍然很少了解Cres中开关样功能是如何编码的，以及特征是如何通过其编码逻辑的变化而进化的。特别是，HOX转录因子代表了一个知之甚少的类别，它为Cres提供了沿主体轴的位置信息。威廉姆斯实验室和瑞贝兹实验室正在合作研究基因和CRE网络，这些基因和CRE负责制造果蝇物种黑腹果蝇雄性特有的身体色素沉着。这一结果将揭示这种色素沉积是如何在果蝇物种的多个谱系中起源和改变的。研究结果将显示HOX基因和Cres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的水平上进行操作。这项工作将提供一幅适用于各种动物系统的特征进化图景。通过这项研究，将改进计算工具，并创建在线学习资源来帮助科学家。这个研究项目将通过高中生、本科生和研究生参与指导性研究来支持科学人员的未来。参与将强调来自科学领域中代表性不足的群体的学生。形成动物身体计划的发育事件被视为新特征进化的熔炉。这个项目的首要目标是了解身体平面图案信息是如何起源于基因调控网络(GRN)的，并随后被修改以使形态特征多样化。GRN的结构是通过将转录因子与顺式调控元件(CRE)结合来控制基因表达来形成模式发展。结合Cre的各种因素的组合形成了一种调控逻辑，它规定了表达的时机、模式和水平。目前，人们对GRN结构如何进化产生不同的表型知之甚少。具体地说，层次结构中的哪些基因被修改，以及最终监管逻辑是如何演变的。威廉姆斯实验室和雷贝兹实验室正在研究GRN的进化及其潜在的调控逻辑，以适应在实验上容易驯服的动物系统中出现的快速进化的特征。拟议的研究将集中在雄性特有的腹部色素沉着模式，这种模式在两个果蝇谱系中一致进化，然后被修改并丢失。第一个目标将描述身体计划的仲裁者(例如，Hox蛋白、辅因子和活性调节剂)如何直接与GRN的Cres相互作用来控制黑腹果蝇中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的色素沉着扩大、收缩或消失的情况下，这种由HOX调控的GRN是如何改变的。第三个目标将追踪GRN如何在非模型苍蝇中独立进化出会聚的色素沉着表型。为了实现这些目标，研究小组将使用包括多个果蝇物种中的报告基因在内的技术，以及转录因子和Cre序列之间的凝胶位移分析，以精确定位表型改变突变，并将这些与它们激发的转录因子结合和功能的变化联系起来。

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.