Integrated computational and experimental study of embryonic patterning by sequential and oscillatory gene regulatory mechanisms

通过顺序和振荡基因调控机制进行胚胎模式的综合计算和实验研究

• 批准号: 418594528
• 负责人: Professor Dr. Martin Klingler, since 9/2022
• 金额: --
• 依托单位: Department Biologie
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2019
• 资助国家: 德国
• 起止时间: 2018-12-31 至 2022-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/418594528?language=en
• 关键词: Integrated; computational; experimental; study; embryonic

Sequential and cyclic waves of gene expression emanating from signaling centers are commonly observed phenomena in embryogenesis (e.g. somitogenesis, neural tube development, and limb development in vertebrates). Recently, I have described cyclic waves of pair-rule, and aperiodic waves of gap gene expression in the posterior organizer region of the beetle Tribolium castaneum. In the proposed project, I use gap and pair-rule gene regulation during the anterior-posterior axis patterning in Tribolium as a simple and tractable model system to study the molecular underpinnings of gene expression waves in development. I take a hypothesis-driven approach, where I test the predictions of a molecular/computational model I recently devised for the regulation of such waves: the "gradual enhancer switching model". In this model, two sets of enhancers are involved in gene regulation: dynamic enhancers and static enhancers. The dynamic enhancers are responsible for the oscillatory/sequential gene expression, and the static enhancer for freezing these waves into stable spatial patterns. Computer models show that such gradual switching (mediated by a morphogen gradient) between these two sets of enhancers can generate gene expression waves. The model is supported by genetic data, but a molecular evidence is still lacking.In the proposed project, I devise reporter assay approaches in live embryos as well as computational approaches to test and modify my models. Detailed analyses of enhancer activities will be carried out in live embryos using the MS2-MCP system in WT and various RNAi knockdown backgrounds. Experimental data will be analyzed and integrated into computational models using in silico evolution techniques.The proposed project expands the current approach of understanding how gene regulatory networks work during development. Interactions between genes are usually viewed as simple activation/repression relationships, and are usually computationally modeled as such. However, recent studies show that a single gene is often regulated by multiple enhancers, forming a complex and dynamic 3D chromatin structures, and driving different expressions that usually overlap in space and time. This complex transcriptional machinery is probably utilized to increase the computational power of gene regulatory networks. My long-term goal is to unravel the computational power of the cis-regulatory machinery within gene regulatory networks in development. In the proposed project, I start with the first tier of complexity, namely the multi-enhancer regulation of genes. In the future, I aim to probe the importance of the 3D chromatin structure of cis-regulatory regions to mediate pattern formation in development.

从信号传导中心发出的基因表达的顺序和循环波是胚胎发生（例如，脊椎动物中的体节发生、神经管发育和肢体发育）中常见的现象。最近，我描述了对规则的周期波，和非周期波的差距基因表达的甲虫赤拟谷盗的后部组织者区域。在拟议的项目中，我使用间隙和配对规则的基因调控在Tribolium的前后轴图案作为一个简单而易于处理的模型系统，研究基因表达波在发展中的分子基础。我采取假设驱动的方法，在那里我测试的分子/计算模型的预测，我最近设计的这种波的调节：“逐步增强开关模型”。在该模型中，两组增强子参与基因调控：动态增强子和静态增强子。动态增强子负责振荡/顺序基因表达，静态增强子负责将这些波冻结为稳定的空间模式。计算机模型显示，这两组增强子之间的这种逐渐切换（由形态发生素梯度介导）可以产生基因表达波。该模型得到了遗传数据的支持，但仍然缺乏分子证据。在拟议的项目中，我设计了活胚胎中的报告分析方法以及计算方法来测试和修改我的模型。增强子活性的详细分析将在WT和各种RNAi敲低背景中使用MS 2-MCP系统在活胚胎中进行。实验数据将被分析并整合到计算机模型中使用在silico evolution techniques.The拟议的项目扩展了目前的方法来理解基因调控网络如何在发展过程中工作。基因之间的相互作用通常被视为简单的激活/抑制关系，并且通常被计算建模为这样。然而，最近的研究表明，单个基因往往受到多个增强子的调控，形成复杂而动态的3D染色质结构，并驱动通常在空间和时间上重叠的不同表达。这种复杂的转录机制可能被用来增加基因调控网络的计算能力。我的长期目标是解开基因调控网络中顺式调控机制的计算能力。在拟议的项目中，我从第一层复杂性开始，即基因的多增强子调控。在未来，我的目标是探索的顺式调控区的三维染色质结构的重要性，以介导模式的形成发展。