Expression, regulation, and role of enhancer RNAs in T helper cells

T 辅助细胞中增强子 RNA 的表达、调控和作用

• 批准号: 8804510
• 负责人: Majid Kazemian
• 金额: $ 24.9万
• 依托单位: PURDUE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-04-01 至 2020-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8804510
• 关键词: Address; Affect; Asses; Asthma; Award; Binding; Binding Proteins; Biological; Biological Assay; Biological Sciences; CD4 Positive T Lymphocytes; Cell Culture Techniques; Cell Differentiation process; Characteristics; Chromatin; Cloning; Complex; Computational Science; Computational Technique; Computer Analysis; Coupled; DNA; DNA Binding; Development Plans; Disease; Education; Educational workshop; Enhancers; Ensure; Equipment; Flow Cytometry; Foundations; Future; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Genome; Genomic DNA; Genomics; Health; Helper-Inducer T-Lymphocyte; High-Throughput Nucleotide Sequencing; Hypersensitivity; Immune; Immune System Diseases; Immune system; Interview; Knowledge; Laboratories; Laboratory Research; Lead; Learning; Libraries; Location; Measures; Mediating; Mentors; Modeling; Monitor; Mus; National Heart, Lung, and Blood Institute; Occupations; Partner in relationship; Pathway interactions; Phase; Play; Population; Preparation; Production; Protocols documentation; RNA; RNA Polymerase II; RNA purification; Regulation; Reporter; Research; Role; STAT protein; Secondary Protein Structure; Signal Pathway; Specific qualifier value; Students; Supervision; Symptoms; T-Cell Development; Techniques; Technology; Time; Training; Transcriptional Regulation; Transfection; Untranslated RNA; adaptive immune response; career development; cell type; cytokine; experimental study; fight against; gene therapy; genetic signature; genome-wide; high throughput screening; improved; knock-down; laboratory experience; mRNA Expression; macrophage; method development; novel; novel strategies; novel therapeutics; pathogen; post-doctoral training; response; skills; spatiotemporal; undergraduate student

DESCRIPTION (provided by applicant): Project Summary/Abstract This K22 proposal describes in detail my plan to obtain the necessary biological and educational skills and apply them in a significant health related subject to develop the foundation of my independent research laboratory. I have obtained an extensive computational training during my undergraduate and graduate studies. I have used these computational skills to improve protein secondary structure prediction, to predict enhancer locations, to model enhancer function, and to uncover regulatory grammar. My one-year postdoctoral training so far, has broadened my view of gene regulation, specifically during T cell development. I have studied noncoding RNAs and their role in T helper cell plasticity and differentiation. Using computational techniques, I have identified several lineage-specific noncoding RNAs in T helper cells. I have started to learn how to perform certain biological experiments to experimentally validate my findings and how to follow certain library preparation protocols. During the mentored phase of this award, I intend to expand my biological skills. To this end, I have tailored my career development plan to include several workshops with laboratory trainings. I have asked my biologist lab-mates to let me observe them performing experiments and to teach and supervise me during certain experiments. I have asked my current advisor to provide me with proper material and equipment to perform experiments. The intended skills that I will master during the mentored phase of this award include real-time PCR, flow cytometry, cell culture and transfection, and high-throughput sequencing library preparation. Obtaining these hands-on biological skills will enable me to setup my ideal mixed dry and wet lab and to effectively mentor graduate and postdoctoral students from both computational and biological sciences. My research plan will address several important biological questions regarding a novel class of noncoding RNAs referred to as enhancer RNAs. It will quantify these noncoding RNAs (Aim1) and characterize their role in T helper cell regulation (Aim2). The regulation of T helper cells is associated with our ability to fight against pathogens, and abnormalities may lead to severe immune diseases. Thus, characterizing novel regulators is important and may open new therapeutic avenues. To ensure the successful completion of this proposal, I have assembled a committee of experts and collaborators that will help me on various aspects of this proposal. Dr. Leonard, an expert in T cell development, will provide me the necessary advice on biological findings. As my primary mentor, he will also provide me the space, equipment, and material needed for the mentored phase of this award. Dr. Jun Zhu, an expert in sequencing technologies, will help me on method development. Dr. Stubbs, an expert in mechanisms of transcriptional regulation, will advice me on the role of enhancer RNAs. Dr. Geller, the director of education at NHLBI, will provide me advice on job search, interview, and transition to the independent phase. Dr. Spolski and Dr. Liao will help me to learn how to perform experiments.

描述（由申请人提供）： 项目摘要/摘要 该 K22 提案详细描述了我的计划，即获得必要的生物学和教育技能并将其应用于重要的健康相关主题，以建立我的独立研究实验室的基础。我在本科和研究生学习期间获得了广泛的计算培训。我利用这些计算技能来改进蛋白质二级结构预测、预测增强子位置、模拟增强子功能以及揭示调控语法。到目前为止，我一年的博士后培训拓宽了我对基因调控的视野，特别是在 T 细胞发育过程中。我研究了非编码 RNA 及其在 T 辅助细胞可塑性和分化中的作用。利用计算技术，我在 T 辅助细胞中鉴定出了几种谱系特异性非编码 RNA。我已经开始学习如何进行某些生物实验来通过实验验证我的发现以及如何遵循某些文库制备方案。在该奖项的指导阶段，我打算扩展我的生物技能。为此，我定制了我的职业发展计划，其中包括多个带有实验室培训的研讨会。我要求我的生物学家实验室伙伴让我观察他们进行实验，并在某些实验期间指导和监督我。我已要求我现在的导师为我提供适当的材料和设备来进行实验。在该奖项的指导阶段，我将掌握的预期技能包括实时 PCR、流式细胞术、细胞培养和转染以及高通量测序文库制备。获得这些生物实践技能将使我能够建立理想的干湿混合实验室，并有效地指导计算科学和生物科学的研究生和博士后学生。我的研究计划将解决有关一类新型非编码 RNA（称为增强子 RNA）的重要生物学问题。它将量化这些非编码 RNA (Aim1) 并表征它们在 T 辅助细胞调节中的作用 (Aim2)。辅助T细胞的调节与我们对抗病原体的能力有关，异常可能导致严重的免疫疾病。因此，表征新型调节剂很重要，并且可能开辟新的治疗途径。为了确保该提案的成功完成，我组建了一个由专家和合作者组成的委员会，他们将在该提案的各个方面为我提供帮助。 Leonard 博士是 T 细胞发育方面的专家，他将为我提供有关生物学发现的必要建议。作为我的主要导师，他还将为我提供该奖项指导阶段所需的空间、设备和材料。测序技术专家朱军博士将帮助我进行方法开发。 Stubbs 博士是转录调控机制方面的专家，他会就增强子 RNA 的作用向我提供建议。 NHLBI 教育总监 Geller 博士将为我提供有关求职、面试和过渡到独立阶段的建议。 Spolski博士和Liao博士将帮助我学习如何进行实验。