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

描述(申请人提供)：转录因子调节特定组织中不同的基因网络，但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动态平衡是极具挑战性的。在这里，我建议利用线虫模型的简单性来研究基因调控网络如何促进发育程序(蜕皮)。我将通过比较线虫的蜕皮网络和人类寄生虫的蜕皮网络来检验这一假设，即自由生活的线虫和寄生线虫之间对蜕皮网络核心元件的核激素受体调节是保守的。自从来到加州大学旧金山分校以来，我获得了特里·福克斯基金会和加拿大卫生研究院的博士后奖学金，因为我探索了核激素受体如何促进线虫的器官发育和先天性免疫。两种核激素受体(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)定义线虫蜕皮网络的组件；ii)定义线虫蜕皮、作用组织和空间调节的功能模块；以及iii)将我的线虫发现推广到人类寄生虫B.marayi。这些目标将通过结合芯片序列、蛋白质组学、数据挖掘、定量遗传分析、基因组编辑和标准线虫技术来实现。将聚焦遗传学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的直接和间接靶标，并确定参与选定的一组蜕皮基因的时间和空间调节的因素。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Nigan Krogan博士(生物信息学分析/编程、质谱学、定量遗传分析)以及我的顾问组成员Alison Frand博士(蜕皮生理学)和Judy Sakanari博士(B.Malayi培养/生理学)那里获得新的培训。我严谨的职业规划和出色而全面的指导团队将使我处于有利地位，能够在美国学术机构获得独立的职位。加州大学旧金山分校享有盛誉的社区精神与其丰富的技术、科学和专业发展资源相结合，将为我开发这个项目并为独立做准备提供一个理想的孵化器。K99/R00赠款将使我能够利用我在线虫核激素受体和基因表达方面的专业知识，使用无偏见的系统方法和专注的遗传学/细胞生物学，在整个动物的背景下研究发育基因调控网络。这项工作将提供对转录网络的结构和进化的洞察，以及对其的扩展 对马来丝虫的了解将为研究蜕皮作为治疗寄生线虫的干预点铺平道路，寄生线虫在全球范围内给29亿人带来负担。

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.