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”）的一个统一特征是其在发育过程中的构建。每个表型性状都需要一系列基因的配合，这些基因的参与由称为顺式调控元件（克雷斯）的DNA序列控制。克雷斯就像开关一样，在特定的生命阶段打开或关闭某些细胞类型的基因。克雷斯的开关样功能在DNA序列中由称为转录因子的蛋白质特异性结合的有序碱基的短片段编码。转录因子的组合形成了一个“逻辑”的指令，精确地确定了哪些细胞，在什么时候CRE可以开关一个基因ON。目前，它仍然知之甚少开关样的功能是如何编码在克雷斯和性状如何演变通过改变其编码的逻辑。特别是，Hox转录因子代表了一个知之甚少的类，它为克雷斯提供了沿身体主轴沿着的位置信息。威廉姆斯和Rebeiz实验室正在合作研究基因和CREs网络，这些基因和CREs负责制造果蝇物种黑腹果蝇的雄性特异性身体色素沉着。这些结果将告知这种色素是如何起源的，以及在果蝇物种的多个谱系中是如何改变的。这些结果将显示一个新特征的构建是如何由Hox基因、克雷斯控制的，以及进化如何在转录因子结合位点的水平上起作用。这项工作将提供一个适用于各种动物系统的性状进化的图片。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。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科学人员的未来。参与将强调来自科学领域代表性不足的群体的学生。动物身体计划的发展事件被认为是新特征进化的熔炉。该项目的首要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），并随后进行修改以使形态特征多样化。GRNs的结构通过转录因子与顺式调控元件（克雷斯）的结合来控制基因表达，从而形成发育模式。结合克雷斯的因子的组合形成指定表达的时间、模式和水平的调节逻辑。目前，很少有人知道GRN结构如何演变，以产生不同的表型。具体来说，层次结构中的哪些基因被修改，以及最终调控逻辑如何演变。威廉姆斯和雷贝兹实验室正在研究GRN的进化及其潜在的调控逻辑，以适应实验上易处理的动物系统中快速进化的特征。拟议的研究将集中在雄性特定的腹部色素沉着模式，在两个果蝇谱系中趋同进化，然后修改和丢失。第一个目标将表征身体计划的仲裁者（例如Hox蛋白、辅因子和活性调节剂）如何直接与GRN的克雷斯相互作用以控制D.黑腹菌第二个目标将确定这种Hox调节的GRN在色素沉着扩大，收缩或在非模型果蝇物种中丢失的情况下如何改变。第三个目标将跟踪这个GRN如何独立地在非模型苍蝇中进化出收敛色素沉着表型。为了实现这些目标，研究小组将采用包括多个果蝇物种中的报告转基因和转录因子与CRE序列之间的凝胶转移测定的技术，以确定表型改变突变，并将这些突变与它们激发的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.