Transcriptional networks controlling molting in C. elegans and B. malayi

描述（由申请人提供）：转录因子调节特定组织中不同的基因网络，然而了解这些网络如何在时间和空间上协调以促进动物发育和体内平衡是极具挑战性的。在这里，我建议研究基因调控网络如何利用模型线虫的简单性来促进发育程序（换毛）。我将通过比较秀丽隐杆线虫和马来人线虫的蜕皮网络，来验证蜕皮网络核心要素的核激素受体调控在自由生活线虫和寄生线虫之间是保守的这一假设。自从来到加州大学旧金山分校，我就因研究核激素受体如何促进秀丽隐杆线虫的器官发育和先天免疫而获得了特里·福克斯基金会和加拿大卫生研究院的博士后奖学金。两个核激素受体（NHR-23和NHR-25）是线虫蜕皮的关键调节因子，我将研究这些转录因子在蜕皮网络中的作用。我建议：I)定义秀丽隐杆线虫蜕皮网络的组成；ii)明确线虫蜕皮的功能模块、作用组织和空间调控；iii)将秀丽隐杆线虫的发现扩展到人类寄生虫马来芽孢杆菌。这些目标将通过ChIP-seq、蛋白质组学、数据挖掘、定量遗传分析、基因组编辑和标准秀丽隐杆线虫技术的结合来实现。将聚焦遗传方法与无偏系统方法相结合，将传递在蜕皮过程中发生变化的基因/蛋白质，确定NHR-23和NHR-25的直接和间接靶点，并确定特定蜕皮基因群的时空调控因素。从长远来看，我将研究完整动物的转录协调机制。为了实现这些目标，我将从我的共同导师Keith Yamamoto博士（ChIP-seq）和Nevan Krogan博士（生物信息学分析/编程，质谱，定量遗传分析）以及我的咨询小组成员Alison Frand博士（换羽生理学）和Judy Sakanari博士（B.马来亚培养/生理学）那里获得新的培训。我严谨的职业规划和优秀全面的导师团队将为我在美国学术机构获得独立职位提供有利条件。UCSF享有盛誉的社区精神，加上其丰富的技术、科学和专业发展资源，将为我开发这个项目和为独立做准备提供理想的孵化器。K99/R00拨款将使我能够利用我在秀丽隐杆线虫核激素受体和基因表达方面的专业知识，使用公正的系统方法和集中的遗传学/细胞生物学，在整个动物的背景下研究发育基因调控网络。这项工作将提供深入了解转录网络的结构和进化，并扩展这一点

DESCRIPTION (provided by applicant): Transcription factors regulate distinct networks of genes in specific tissues, yet understanding how these networks are coordinated temporally and spatially to promote animal development and homeostasis is extremely challenging. Here, I propose to study how gene regulatory networks promote a developmental program (molting) using the simplicity of the model nematode C. elegans. I will test the hypothesis that nuclear hormone receptor regulation of core elements of the molting network are conserved between free-living and parasitic nematodes by comparing the C. elegans molt network to that of the human parasite, B. malayi. Since arriving at UCSF, I have been awarded both Terry Fox Foundation and Canadian Institutes of Health postdoctoral fellowships for work that explored how nuclear hormone receptors promote organ development and innate immunity in C. elegans. Two nuclear hormone receptors (NHR-23 and NHR-25) are key regulators of C. elegans molting, and I will investigate the roles of these transcription factors in the molting network. Hee I propose to: i) define the components of the C. elegans molting network; ii) define functional modules in the C. elegans molt, tissues of action and spatial regulation; and iii) extend my C. elegans findings into the human parasite, B. malayi. These aims will be achieved through a combination of ChIP-seq, proteomics, data mining, quantitative genetic analysis, genome editing, and standard C. elegans techniques. Combining the focused genetic approach with an unbiased systems approach will deliver genes/proteins that change during the molt, identify direct and indirect targets of NHR-23 and NHR-25, and determine the factors involved in temporal and spatial regulation of select groups of molting genes. In the long-term, I will investigate the mechanisms of transcriptional coordination in an intact animal. To achieve these aims, I will acquire new training from my co-mentors Dr. Keith Yamamoto (ChIP-seq) and Dr. Nevan Krogan (bioinformatics analysis/ programming, mass spectrometry, quantitative genetic analysis), and from my Advisory Group members Dr. Alison Frand (molting physiology) and Dr. Judy Sakanari (B. malayi culture/physiology). My rigorous career plan, and outstanding and comprehensive mentoring team will put me in a strong position to secure an independent position in a U.S. academic institution. The renowned community spirit of UCSF combined with its rich technical, scientific, and professional development resources will provide an ideal incubator for me to develop this project and prepare for independence. A K99/R00 grant will allow me to build on my expertise in C. elegans nuclear hormone receptors and gene expression, using both unbiased systems approaches and focused genetics/cell biology, to study developmental gene regulatory networks in the context of an entire animal. This work will provide insight into the structure and evolution of transcriptional networks, and extension of this knowledge to B. malayi will pave the way for investigations into molting as an intervention point in treating parasitic nematodes, which burden 2.9 billion people globally.