Mapping network connectivity within zebrafish segmentation clock and wavefront

映射斑马鱼分段时钟和波前的网络连接

• 批准号: 8636711
• 负责人: SCOTT A HOLLEY
• 金额: $ 24.98万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-21 至 2015-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8636711
• 关键词: Affinity; Algorithms; Anterior; Binding; Biochemical; Biological Process; Cells; Chromatin; Complement; Complex; Congenital Disorders; DNA; DNA Binding; Data; Data Set; Development; Diabetes Mellitus; Drug Interactions; Drug Targeting; Dysostoses; Exhibits; Family; Fibroblast Growth Factor; Fluorescent in Situ Hybridization; Gene Expression; Gene Targeting; Genes; Genetic; Genetic Transcription; Grant; Human; In Situ Hybridization; Knowledge; Lead; Light; Maps; Measurement; Measures; Messenger RNA; Methodology; Methods; Metric; Modeling; Modification; Mus; Mutation; Network-based; Noise; Organism; Output; Pathway interactions; Pattern; Performance; Phenotype; Property; Proteins; Regulation; Repression; Role; Segmentation Clock Pathway; Signal Pathway; Signal Transduction; Simulate; Structure; System; Testing; Time; Tissues; Zebrafish; design; dimer; disease phenotype; improved; in vivo; insight; interest; knock-down; malformation; mathematical model; member; network models; public health relevance; response; rib bone structure; somitogenesis; spine bone structure; trait; transcription factor

DESCRIPTION (provided by applicant): Segmentation of the vertebrate anterior-posterior axis is dependent on oscillations of her/he's genes. In humans, mutation of HES7 results in spondylocostal dysostosis, a congenital disorder characterized by fusion or malformation of the vertebrae and ribs. Within the zebrafish segmentation clock, six members of the her/hes family form both hetero- and homodimers and negatively regulate their own transcription. Even within this simple network, there are 36 possible dimer-DNA interactions and, given 3 levels of repression, 1017 possible network topologies. Previous models of gene networks based on transcription factor (TF) binding included data on binding affinities, cell-specific protein concentrations and chromatin accessibility. However, TF binding may not always lead to significant changes in transcription and in many cases biochemical data may be incomplete. Here, a method for determining transcription factor networks that does not need extensive biochemical datasets will be developed. Mapping the network will rely on gene knockdown and quantitative measurement of transcription combined with mathematical modeling and global optimization algorithms. Predictions derived from the network model will be tested experimentally via compound gene knockdown, qPCR and in situ hybridization. Network-based explanations for several incongruous phenotypes will be attained. Lastly, modeling these interactions will be used to shed light on how networks can evolve between species or within an organism to complete a different task with minimal modifications. Understanding gene networks, such as the segmentation clock studied here, enables modeling of biological processes. These models can lead to identification of nodes of cellular pathways, the role of multiple genes in disease phenotypes, and insight into drug interactions.

描述（由申请人提供）：脊椎动物前轴的分割取决于其基因的振荡。在人类中，HES7的突变导致脊柱脊髓病，这是一种以椎间和肋骨融合或畸形为特征的先天性疾病。在斑马鱼的分段时钟内，HE/HES家族的六名成员形成异二聚体和同型二聚体，并对自己的转录进行负调节。即使在这个简单的网络中，也存在36个可能的二聚体-DNA相互作用，并且在3个级别的抑制级别上，可能是1017个可能的网络拓扑。 基于转录因子（TF）结合的基因网络的先前模型包括有关结合亲和力，细胞特异性蛋白质浓度和染色质可及性的数据。但是，TF结合可能并不总是会导致转录发生重大变化，在许多情况下，生化数据可能不完整。在这里，将开发一种不需要大量生化数据集的转录因子网络的方法。映射网络将依靠基因敲低和转录的定量测量与数学建模和全局优化算法相结合。从网络模型中得出的预测将通过化合物基因敲低，qPCR和原位杂交进行实验测试。将获得基于网络的基于网络的解释，以实现几种不协调的表型。 最后，对这些相互作用进行建模将用于阐明网络如何在物种之间或生物体内的发展，以最少的修改完成另一个任务。 了解基因网络，例如此处研究的分割时钟，可以对生物过程进行建模。这些模型可以导致鉴定细胞途径的节点，多个基因在疾病表型中的作用以及对药物相​​互作用的见解。