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: 8878398
• 负责人: LIN CHEN
• 金额: $ 32.9万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-08-01 至 2014-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8878398
• 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; Complex; Coupled; DNA; DNA Binding; Data; Development; Disease; Distal; Ectopic Expression; Epigenetic Process; Equilibrium; Gene Expression; Gene Expression Regulation; Gene Targeting; Genes; Genetic Transcription; Genome; Goals; Graft Rejection; Homeostasis; Immune; Immune system; Immunity; Immunosuppression; Immunotherapy; Inflammatory; Knowledge; Leucine Zippers; Link; Malignant Neoplasms; Mediating; Methods; Molecular; Molecular Conformation; Molecular Profiling; N-terminal; Other Genetics; Play; Proline; Protein Family; Regulatory T-Lymphocyte; Research; Resolution; Role; Self Tolerance; Site; Solutions; Structure; System; T-Lymphocyte; T-Lymphocyte Subsets; Technology; Testing; Therapeutic; Transcriptional Regulation; Zinc Fingers; autoreactive T cell; base; cancer immunotherapy; dimer; gene interaction; genome-wide; in vitro testing; in vivo; insight; loss of function; loss of function mutation; programs; public health relevance; transcription factor

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 suppresses 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 (e.g. transplantation rejection) 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 reveal 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 adress 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 basis of DNA bridging by FOXP3 by determining the structures of FOXP3 bound to DNA and its higher-order oligomer complex. Aim 2 is to test if FOXP3 can directly bridge DNA at the biochemical level and if FOXP3 can regulates long distance gene-gene interactions inside 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(由申请者提供)：探索FOXP3在基因组三维组织中的S角色。Foxp3是一种转录因子，在调节性T细胞(Treg)中表达，对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功能丧失突变很容易被认为是自身免疫性疾病。FOXP3在Treg的发育和功能中的关键作用以及利用Treg为基础的治疗(如移植排斥)的潜力引起了人们对FOXP3的基本作用机制的极大关注。对FOXP3结合位点的全基因组分析(芯片上芯片和芯片序列)与表达谱相结合，揭示了数千个潜在的FOXP3激活或抑制基因。虽然这些基因中的一些后来被证明对Treg很重要，但FOXP3介导的基因表达和Treg功能之间的机制理解仍然缺乏。这项拟议的研究旨在通过探索FOXP3在基因组3D组织中的S角色来解决这个问题。以往对FOXP3的结构/功能研究表明，Tregs的抑制功能需要一种意想不到的结构域交换机制。初步证据表明，结构域互换的FOXP3二聚体可能已经进化成桥接DNA，从而介导染色质的长距离相互作用。这种转录调控模式早已被认识到，并在最近几年得到了相当大的关注，但远距离染色质相互作用的分子基础尚未得到表征。Foxp3为解决这个问题提供了一个理想的系统，这反过来又可以深入了解FOXP3在Treg中的机械作用。拟议的研究有以下三个具体目标。目的1通过测定与DNA结合的FOXP3及其高阶低聚物复合体的结构来表征FOXP3桥联DNA的结构基础。目的2检测FOXP3是否能直接在生化水平上桥接DNA，以及FOXP3是否能调节细胞内基因与基因的长距离相互作用。目的3是利用一种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。拟议的研究试图推进FOXP3如何通过基因组3D结构的全球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在Treg中的抑制作用机制提供新的视角，并有助于以Treg为基础的自身免疫性/炎症性疾病治疗和癌症免疫治疗的发展。