Dissecting expression divergence in developmental networks across Drosophilids

剖析果蝇发育网络中的表达差异

• 批准号: 8535183
• 负责人: Zeba B Wunderlich
• 金额: $ 12.88万
• 依托单位: HARVARD MEDICAL SCHOOL
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-01 至 2015-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8535183
• 关键词: Adult; Affect; Amino Acid Sequence; Animal Experiments; Animal Husbandry; Animals; Anterior; Atlases; Award; Biological Models; Biology; Blastoderm; Cells; Chromatin Structure; Code; Comparative Study; Competence; Complex; Computational Biology; Computational Technique; Computing Methodologies; DNA; Data; Data Set; Defect; Development; Developmental Gene; Developmental Process; Distant; Doctor of Philosophy; Drosophila genus; Drosophila melanogaster; Elements; Embryo; Enhancers; Environment; Evolution; Faculty; Fellowship; Fostering; Foundations; Gene Combinations; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Genes; Genetic Transcription; Genome; Grant; Hour; Image; Imaging Techniques; Individual; Lead; Location; Masks; Mathematics; Measurement; Measures; Mechanics; Mentors; Methods; Microscopy; Mining; Modeling; Molecular Profiling; Muscle Cells; Mutation; Neurons; Orthologous Gene; Outcome; Output; Pattern; Peptide Sequence Determination; Phase; Photons; Phylogenetic Analysis; Physics; Postdoctoral Fellow; Regulator Genes; Regulatory Element; Research; Research Personnel; Resolution; Resources; Scheme; Specific qualifier value; Structure-Activity Relationship; Students; Systems Biology; Testing; Time; Training; Transcription Initiation Site; Transcriptional Regulation; Transgenic Animals; Transgenic Organisms; Universities; Untranslated Regions; Work; cell type; genome sequencing; image processing; interest; mature animal; member; post-doctoral training; programs; promoter; research study; spatiotemporal; success; transcription factor; zygote

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.

描述（由申请人提供）：当单个细胞分裂并在成人中产生多种细胞类型时，发育过程由复杂的时空基因表达模式指导，其由转录网络控制。该提案使用指定果蝇胚胎中前后轴的转录网络作为模型系统，以探索调控回路如何在基因组中编码以及它们如何在物种之间变化。动物中的基因表达受转录因子（TF）、顺式调节元件（克雷斯，也称为增强子）、核心启动子、非翻译区（UTR）、调节RNA、沉默子、绝缘子和染色质结构之间的相互作用控制。据认为，核心启动子元件和染色质结构在转录起始位点提供转录的一般能力，而更远的克雷斯在特定条件下上调基因的表达。我们缺乏一个完整的框架，使我们能够测量和理解网络联合收割机的不同组成部分的变化如何结合起来，以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，但使用我们灵敏的成像技术，我们观察到这些不同种类的果蝇之间的基因表达模式的时间和空间位置的许多定量变化。利用我们对5种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的贡献（例如，克雷斯，启动子）的表达差异，我们观察到物种之间。这一奋进的成功将使我们更好地理解序列差异如何干扰早期发育的某些方面，同时保护其他方面，并将告知我们对克雷斯，启动子和其他调控元件的结构-功能关系的理解。 该项目的PI，Wunderlich博士，旨在将她在计算生物学方面的研究生培训与她在实验果蝇系统生物学方面的博士后培训相结合，为一个独立的研究实验室奠定基础，该实验室将使用实验和计算技术相结合的方法来研究指导发育的基因调控网络如何在基因组中编码。在这里，我建议在我博士后培训的剩余时间内完成一个数据集和初始计算分析，这将促进我自己实验室的大量后续研究。由哈佛大学系统生物学系提供的环境是唯一适合这种培训，因为它是由教师，博士后研究员，学生和其他研究人员具有各种背景，从生物学到数学到物理学。这种跨学科的环境，重点是定量方法在生物学中的应用，非常符合我的兴趣，并为开展这里提出的工作提供了支持性的环境。该部门和大学有一些教师的利益与我的重叠，也提供了畜牧业，显微镜，计算和行政资源，将使这个项目。

项目成果

Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection.

遗传变异分析表明 DNA 形状参与纯化选择。

• DOI: 10.1093/molbev/msy099
• 发表时间: 2018
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Wang,Xiaofei;Zhou,Tianyin;Wunderlich,Zeba;Maurano,MatthewT;DePace,AngelaH;Nuzhdin,SergeyV;Rohs,Remo
• 通讯作者: Rohs,Remo