Addressing the precision-plasticity paradox in metazoan gene regulatory networks

这个项目试图发现细胞内和环境信号如何改变DNA结合蛋白激活的基因谱系。在特定的细胞、发育和生理环境中，DNA结合蛋白通常以精确的方式控制特定的靶基因网络。然而，细胞或细胞外条件的变化可以增加蛋白质-DNA相互作用的可塑性，从而使一组完全不同的基因成为靶标。这种从精确到可塑性的转变可能是多细胞生物体(如人类)正常发展的关键，剖析其潜在机制可能会提高我们对生物如何在面临环境波动时保持健康的理解。除预期的科学成就外，解决这一研究问题将加强和丰富科学事业，为两名女科学家和一批本科生，包括那些代表性不足的少数群体提供培训和教育机会。这项研究中使用的经典和最先进的遗传学和分子方法将作为对初出茅庐的科学家的教育的激动人心的刺激，以及为那些选择其他职业道路的人的教育提供一个推理和解决问题的概念框架。本研究的长期目标是了解在多细胞真核生物中产生基因转录调节的显著特异性的分子机制。基于该实验室以前的工作，出现了一个两部分模型，根据该模型，给定的DNA结合转录调节因子(TF)可以精确地调节一组特定的基因靶点，或者在促进可塑性的条件下，调节一组完全不同的基因。该模型认为，细胞内或细胞外信号创造了一个特定的背景，该背景支配着TF将如何与其他DNA结合和非DNA结合的协同调节因子相关联，以激活不同的基因靶点网络。这一模型将在线虫秀丽线虫身上进行测试，该线虫具有独特的特征，包括紧凑的基因组、在完整生物体中进行方便的时空分析、强大的遗传学以及包括CRISPR/Cas9基因组编辑在内的一整套基因组学工具。这项研究将集中在核激素受体Tf，NHR-25的精确和可塑性作用上。先前的结果表明，相邻细胞中NHR-25活性的梯度--通过蛋白质翻译后差异相加(SUMO)建立--驱动着不同的基因网络，从而导致独特的细胞命运和随后的组织分化和器官发生。转录网络控制的复杂性将通过实验解决：定义和分析细胞上下文依赖的NHR-25-SUMO调控网络；识别使NHR-25调控可塑性的途径和机制；以及为enChIP分析准备材料，以确定与NHR-25依赖的反应元件相关的蛋白质。所获得的结果将与后生动物转录调控广泛相关，并为未来基因调控的研究提供重要的基础。

This project seeks to discover how intracellular and environmental signals change the repertoire of genes activated by DNA-binding proteins. In a particular cellular, developmental and physiological context, DNA-binding proteins normally operate with precision to control a specific network of target genes. However, changes in cellular or extracellular conditions can increase the plasticity of protein-DNA interactions, such that an entirely different group of genes is targeted. This kind of switch from precision to plasticity may hold the key to proper development in multicellular organism, like humans, and dissecting the underlying mechanisms may improve our understanding of how organisms maintain their well-being in the face of environmental fluctuation. In addition to the expected scientific achievements, tackling this research problem will strengthen and enrich the scientific enterprise by providing training and educational opportunities for two women scientists and for a cohort of undergraduate students, including those who are underrepresented minorities. Classic and state-of-art genetic and molecular approaches used in this project will serve as exciting stimuli for the education of budding scientists, as well as a conceptual framework for reasoning and problem solving for the education of those who choose other career paths.The long-term goal of this research is to understand the molecular mechanisms that generate the remarkable specificity with which gene transcription is regulated in multicellular eukaryotes. Based on prior work in this laboratory, a bipartite model has emerged whereby a given DNA-binding transcriptional regulatory factor (TF) can either operate precisely to regulate a specific set of gene targets or, under conditions that promote plasticity, operate to regulate an entirely different set of genes. The model contends that intra- or extracellular signals create a specific context that governs how the TF will associate with other DNA-binding and non-DNA-binding coregulatory factors to activate distinct networks of gene targets. This model will be tested in the nematode, Caenorhabditis elegans, which offers unique features including a compact genome, facile spatiotemporal analyses in the intact organism, powerful genetics, and a comprehensive suite of genomics tools, including CRISPR/Cas9 genome editing. The research will focus on the precise vs. plastic action of the nuclear hormone receptor TF, NHR-25. Previous results showed that a gradient of NHR-25 activity--set up by differential post-translational sumoylation (SUMO) of the protein--in neighboring cells drives distinct gene networks that result in unique cell fates and subsequent tissue differentiation and organogenesis. The complexity of transcription network control will be addressed experimentally to: define and analyze cell-context dependent NHR-25-SUMO regulatory networks; identify pathways and machineries that enable NHR-25 regulatory plasticity; and prepare materials for enChIP analysis to identify proteins associating at NHR-25 dependent response elements. The results obtained will be broadly relevant to metazoan transcriptional regulation and provide an important foundation for future studies of gene regulation.