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

合作研究：解决导致 Hox 调控性状重复进化的基因调控网络改变

• 批准号: 1555906
• 负责人: Thomas Williams
• 金额: $ 83.88万
• 依托单位: University of Dayton
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-01 至 2021-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1555906&HistoricalAwards=false
• 关键词: Collaborative; Research; Resolving; gene; regulatory

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.

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造。每个表型性状都需要一组基因的合作，这些基因的参与由称为顺式调控元件（CRE）的 DNA 序列控制。 CRE 的作用就像开关一样，可以在特定生命阶段的某些细胞类型中打开或关闭基因。 CRE 的类似开关功能是由短段有序碱基在 DNA 序列中编码的，称为转录因子的蛋白质与这些碱基特异性结合。转录因子的组合形成指令的“逻辑”，精确地确定 CRE 可以在哪些细胞以及何时开启基因。目前，人们对类似开关的功能如何在 CRE 中编码以及特征如何通过其编码逻辑的变化而演变仍然知之甚少。特别是，Hox 转录因子代表了一个人们知之甚少的类别，它为 CRE 提供沿着身体主轴的位置信息。 Williams 和 Rebeiz 实验室正在合作研究基因和 CRE 网络，这些基因和 CRE 负责使果蝇物种果蝇产生雄性特有的身体色素沉着。研究结果将揭示这种色素沉着是如何在果蝇物种的多个谱系中起源和改变的。结果将展示新特征的构建如何由 Hox 基因、CRE 控制，以及进化如何在转录因子结合位点水平上进行。这项工作将提供适用于多种动物系统的性状进化图景。通过这项研究，将完善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。参与将重点关注来自科学领域代表性不足群体的学生。动物身体计划的发育事件被视为新特征进化的考验。该项目的首要目标是了解身体规划图案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。 GRN 的结构是通过转录因子与顺式调控元件 (CRE) 结合来控制基因表达来形成发育模式。结合 CRE 的因素组合形成了规定表达时间、模式和水平的调控逻辑。目前，人们对 GRN 结构如何进化以产生不同表型知之甚少。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。 Williams 和 Rebeiz 实验室正在研究 GRN 的进化及其潜在的调节逻辑，以适应实验上易处理的动物系统中存在的快速进化的特征。拟议的研究将重点关注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共同进化，然后被修改和丢失。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 CRE 相互作用，以控制黑腹果蝇色素沉着酶的表达模式。第二个目标将确定在非模型果蝇物种色素沉着扩大、收缩或消失的情况下，这种 Hox 调节的 GRN 如何改变。第三个目标是追踪这个 GRN 如何在非模型果蝇中独立进化出趋同的色素沉着表型。为了实现这些目标，研究小组将采用多种技术，包括在多个果蝇物种中进行报告基因转基因，以及转录因子和 CRE 序列之间的凝胶位移测定，以查明改变表型的突变，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。 。