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（应用程序提供）：探索Foxp3在基因组3D组织中的作用。 FOXP3是在调节性T细胞（Treg）中表达的转录因子，这对于免疫系统的平衡功能至关重要。 Treg抑制自动反应性T细胞的活性； FOXP3的功能丧失突变有时会受到自身免疫性疾病的喜好。 FOXP3在Tregs的开发和功能以及利用基于Treg的疗法的潜力的关键作用引起了人们对Foxp3的基本功能机制的极大关注。对FOXP3结合位点（芯片和芯片seq）的全基因组分析与表达分析结合显示了数千个潜在的Foxp3激活或反射基因。尽管这些基因中的一些随后被证明对Treg很重要，但FOXP3介导的基因表达与Treg功能之间的机械理解仍然缺乏。拟议的研究旨在通过探索Foxp3在基因组的3D组织中的作用来解决这个问题。 FOXP3的先前结构/功能研究揭示了Treg抑制功能所需的意外域交换机制。初步证据表明，结构域交换的Foxp3二聚体可能已经演变为桥接DNA，从而介导了远程染色质相互作用。近年来，这种转录调节方式长期以来已被认识并获得了考虑，但是尚未表征长距染色质相互作用的分子基础。 FOXP3提供了一个理想的系统来解决此问题，进而可以洞悉Tregs中Foxp3的机械作用。拟议的研究具有以下三个具体目标。目的1是通过确定与DNA结合的FOXP3结构及其高阶低聚物复合物的结构来表征FOXP3桥接DNA的结构碱基和分子细节。 AIM 2是分析FOXP3在生化水平上的溶液中桥接的DNA桥接，并测试FOXP3桥接是否与细胞中的长距离基因相互作用相关。 AIM 3是使用新开发的染色体会议捕获技术探索FOXP3对T细胞基因组全球架构的影响。拟议的研究旨在通过基因组的3D结构的全球重组来调节FOXP3如何调节特定基因表达的基本知识。这些研究将提供一个新的角度来研究FOXP3在Treg中赋予抑制功能的机制，并有助于开发基于Treg的自身免疫/炎症性疾病和癌症免疫疗法的疗法。