Explore FOXP3's role in the 3D organization of the genome

探索 FOXP3 在基因组 3D 组织中的作用

• 批准号: 9197263
• 负责人: LIN CHEN
• 金额: $ 41.25万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-01-01 至 2019-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9197263
• 关键词: Address; Alanine; Architecture; Attention; Autoimmune Diseases; Autoimmune Process; Autoimmunity; Binding; Binding Sites; Biochemical; Biological Assay; Candidate Disease Gene; Cell Lineage; Cells; ChIP-on-chip; ChIP-seq; Chromatin; Chromosomes; Complement; Complex; Coupled; Crystallization; DNA; DNA Binding; DNA analysis; Data; Development; Dimensions; Dimerization; Disease; Distal; Epigenetic Process; FOXP1 gene; FOXP3 gene; Gene Expression; Gene Expression Regulation; Gene Targeting; Genes; Genetic Transcription; Genome; Goals; Homeostasis; Immune; Immunity; Immunosuppression; Immunotherapy; Inflammatory; Knowledge; Leucine Zippers; Link; Malignant Neoplasms; Mediating; Molecular; Molecular Profiling; Mutagenesis; N-terminal; Other Genetics; Play; Proline; Protein Family; Regulatory T-Lymphocyte; Research; Role; Self Tolerance; Site; Structure; System; T-Lymphocyte; T-Lymphocyte Subsets; Technology; Testing; Therapeutic; Transcriptional Regulation; Zinc Fingers; autoreactive T cell; base; cancer immunotherapy; chromosome conformation capture; dimer; gene interaction; genome-wide analysis; immune self tolerance; immune system function; in vivo; insight; loss of function; loss of function mutation; programs; public health relevance; transcription factor; whole genome

 DESCRIPTION (provided by applicant): Explore FOXP3's role in the 3D organization of the genome. FOXP3 is a transcription factor expressed in regulatory T cells (Tregs) that are essential for the balanced function of the immune system. Tregs suppress the activity of autoreactive T cells; loss-of-function mutations in FOXP3 are casually liked to autoimmune diseases. The critical role of FOXP3 in the development and function of Tregs and the potential to harness Treg-based therapies have attracted much attention to the basic functional mechanism of FOXP3. Genome-wide analyses of FOXP3 binding sites (ChIP-on-chip and ChIP-seq) coupled with expression profiling revealed thousands of potential FOXP3- activated or repressed genes. Although some of these genes have subsequently been shown to be important to Treg, a mechanistic understanding between FOXP3-mediated gene expression and Treg function is still lacking. The proposed research intends to address this question by exploring FOXP3's role in the 3D organization of the genome. Previous structure/function studies of FOXP3 reveal an unexpected domain-swapping mechanism that is required for the suppression function of Tregs. Preliminary evidence suggests that the domain-swapped FOXP3 dimer may have evolved to bridge DNA, thereby mediating long-range chromatin interactions. This mode of transcription regulation has long been recognized and has gained considerable attention in recent years, but the molecular basis underlying the long-distance chromatin interactions has not been characterized. FOXP3 provides an ideal system to address this question, which in turn can yield insights into the mechanistic roles of FOXP3 in Tregs. The proposed research has the following three specific aims. Aim 1 is to characterize the structural bases and molecular details of DNA bridging by FOXP3 by determining the structures of FOXP3 bound to DNA and its higher-order oligomer complex. Aim 2 is to analyze DNA bridging by FOXP3 in solution at the biochemical level and test if DNA bridging by FOXP3 correlates with long distance gene-gene interactions in cells. Aim 3 is to explore the effects of FOXP3 on the global architecture of the T cell genome using a newly developed chromosome conformation capture technology. The proposed studies seek to advance basic knowledge on how FOXP3 regulates specific gene expression via global reorganization of the 3D architecture of the genome. These studies will provide a new angle to study the mechanism by which FOXP3 confers the suppression function in Tregs and aid the development of Treg-based therapies in autoimmune/inflammatory diseases and immunotherapy of cancer.

 描述（由申请人提供）：探索 FOXP3 在基因组 3D 组织中的作用。 FOXP3 是一种在调节性 T 细胞 (Treg) 中表达的转录因子，对于免疫系统的平衡功能至关重要。 Tregs 抑制自身反应性 T 细胞的活性； FOXP3 的功能丧失突变很容易导致自身免疫性疾病。 FOXP3 在 Tregs 的发育和功能中的关键作用以及利用基于 Treg 的疗法的潜力引起了人们对 FOXP3 基本功能机制的广泛关注。对 FOXP3 结合位点（ChIP-on-chip 和 ChIP-seq）的全基因组分析以及表达谱分析揭示了数千个潜在的 FOXP3 激活或抑制基因。尽管其中一些基因随后被证明对 Treg 很重要，但 FOXP3 介导的基因表达和 Treg 功能之间的机制仍然缺乏理解。拟议的研究旨在通过探索 FOXP3 在基因组 3D 组织中的作用来解决这个问题。先前对 FOXP3 的结构/功能研究揭示了一种意想不到的域交换机制，这是 Treg 抑制功能所必需的。初步证据表明，结构域交换的 FOXP3 二聚体可能已经进化为桥接 DNA，从而介导长程染色质相互作用。这种转录调控模式早已被认识，并近年来引起了相当大的关注，但长距离染色质相互作用的分子基础尚未被表征。 FOXP3 提供了一个理想的系统来解决这个问题，进而可以深入了解 FOXP3 在 Tregs 中的机制作用。拟议的研究有以下三个具体目标。目标 1 是通过确定与 DNA 结合的 FOXP3 及其高阶寡聚物复合物的结构来表征 FOXP3 桥接 DNA 的结构基础和分子细节。目标 2 是在生化水平上分析溶液中 FOXP3 的 DNA 桥接，并测试 FOXP3 的 DNA 桥接是否与细胞中的长距离基因间相互作用相关。目标 3 是利用新开发的染色体构象捕获技术探索 FOXP3 对 T 细胞基因组整体结构的影响。拟议的研究旨在增进有关 FOXP3 如何通过基因组 3D 结构的全局重组来调节特定基因表达的基础知识。这些研究将为研究FOXP3赋予Tregs抑制功能的机制提供新的视角，并有助于开发基于Tregs的自身免疫/炎症性疾病和癌症免疫治疗疗法。