Dissecting expression divergence in developmental networks across Drosophilids

描述(申请人提供)：当单个细胞在成人中分裂并产生多种细胞类型时，发育过程由错综复杂的时空基因表达模式指导，这些模式由转录网络控制。这项建议使用指定果蝇胚胎前后轴的转录网络作为模型系统，来探索基因组中调控电路是如何编码的，以及它们在物种之间是如何变化的。动物的基因表达受转录因子、顺式调控元件、核心启动子、非翻译区、调控RNA、沉默因子、绝缘体和染色质结构之间的相互作用控制。人们认为核心启动子元件和染色质结构提供了转录起始点的一般转录能力，而较远的Cres在特定条件下上调基因的表达。我们缺乏一个完整的框架来衡量和理解网络不同组成部分的变化如何结合在一起来维持或改变个体或物种之间的输出基因表达水平。控制果蝇前后轴形成的调控网络是高度保守的，然而利用我们敏感的成像技术，我们观察到这些不同物种果蝇之间基因表达模式的时间和空间位置的许多定量变化。使用我们对5个密切相关的果蝇物种的基因表达模式的精确测量、计算方法和互补的转基因动物实验，我们将确定调控网络的不同组成部分(例如，Cres、启动子)对我们观察到的物种间表达差异的贡献。这一努力的成功将使我们更好地理解序列差异如何在保护其他方面的同时扰乱早期发育的某些方面，并将有助于我们理解CRE、启动子和其他调控元件的结构-功能关系。这个项目的私人助理温德利希博士的目标是，将她在计算生物学方面的研究生培训和在实验果蝇系统生物学方面的博士后培训结合起来，为建立一个独立的研究实验室奠定基础，该实验室将结合实验和计算技术，研究指导发育的基因调控网络是如何在基因组中编码的。在这里，我建议在我剩余的博士后培训期间完成一个数据集和初步的计算分析，这将促进我自己的实验室进行大量后续研究。哈佛大学系统生物学系提供的环境特别适合这种培训，因为它由教职员工、博士后研究员、学生和其他研究人员组成，他们具有从生物学到数学再到物理的各种背景。这种跨学科的环境，重点是定量方法在生物学中的应用，与我的兴趣非常匹配，并为开展这里提出的工作提供了一个有利的环境。该部门和大学有许多教职员工的兴趣与我重叠，并提供畜牧学、显微镜、计算和管理资源，使这个项目成为可能。 与公共健康相关：在发育过程中，受精卵会多次分裂，产生形成成年动物的细胞。为了创造不同的细胞类型，例如神经元和肌肉细胞，每个细胞在不同的发育阶段表达特定水平的不同基因组合，该程序中的错误可能导致发育缺陷。这项建议旨在了解有关发育基因表达计划的信息是如何在基因组中编码的，并了解基因组序列的变化如何影响基因表达的模式。

DESCRIPTION (provided by applicant): As a single cell divides and gives rise to multiple cell types in the adult, the developmental process is directed by intricate spatio-temporal gene expression patterns, which are controlled by transcriptional networks. This proposal uses the transcriptional network that specifies the anterior-posterior axis in Drosophila embryos as a model system to explore how regulatory circuits are encoded in the genome and how they change between species. Gene expression in animals is controlled by the interaction between transcription factors (TFs), cis-regulatory elements (CREs, also called enhancers), core promoters, untranslated regions (UTRs), regulatory RNAs, silencers, insulators, and chromatin structure. It is thought that core promoter elements and chromatin structure provide general competence for transcription at transcription start sites, while more distant CREs up-regulate expression of genes under specific conditions. We lack a complete framework that allows us to measure and understand how changes in different components of the network combine to maintain or alter output gene expression levels between individuals or species. The regulatory network that controls Drosophila anterior-posterior axis formation is highly conserved, yet using our sensitive imaging techniques, we observe many quantitative changes in the timing and spatial location of gene expression patterns between these different species of Drosophila. Using our precise measurements of gene expression patterns in 5 closely related Drosophila species, computational methods, and complementary transgenic animal experiments, we will determine the contributions of different components of the regulatory network (e.g., CREs, promoters) to the expression divergence we observe between species. Success in this endeavor will lead to a better understanding of how sequence divergence perturbs some aspects of early development while conserving others and will inform our understanding of the structure-function relationship of CREs, promoters, and other regulatory elements. The PI for this project, Dr. Wunderlich, aims to combine her graduate training in computational biology with her postdoctoral training in experimental Drosophila systems biology to lay the foundation for an independent research lab that will use a combination of experimental and computational techniques to study how the gene regulatory networks that direct development are encoded in the genome. Here I propose to complete a data set and initial computational analyses during the remainder of my postdoctoral training that will foster a large set of subsequent studies in my own lab. The environment provided by the Harvard University Systems Biology Department is uniquely suitable for this training, as it is comprised of faculty members, postdoctoral fellows, students and other researchers with a variety of backgrounds from biology to mathematics to physics. This interdisciplinary environment, with a focus on the application of quantitative methods to biology, is well-matched to my interests and provides a supportive environment for undertaking the work proposed here. The department and university has a number of faculty members with interests that overlap with mine and also provides the animal husbandry, microscopy, computational and administrative resources that will enable this project. PUBLIC HEALTH RELEVANCE: During development, a fertilized egg divides many times to create the cells that will form the adult animal. To create different cell types, e.g. neurons and muscle cells, each cell expresses different combinations of genes at particular levels during different phases of development, and errors in this program can cause defects in development. This proposal aims to understand how information about this developmental gene expression program is encoded in the genome and to understand how changes in the genome sequence affect the patterns of gene expression.