Topological Control of Antigen Receptor Loci during Lymphocyte Development

淋巴细胞发育过程中抗原受体位点的拓扑控制

• 批准号: 9447778
• 负责人: CRAIG H BASSING
• 金额: $ 81.79万
• 依托单位: CHILDREN'S HOSP OF PHILADELPHIA
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-25 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9447778
• 关键词: Antigen Receptors; Architecture; Binding; Boundary Elements; Cell Nucleus; Chromatin; Clinical Management; Collaborations; Communication; Consensus; DNA; Data; Defect; Development; Disease; Elements; Enhancers; Event; Foundations; Gene Expression; Gene Expression Regulation; Genes; Genetic Recombination; Genetic Transcription; Genome; Human Genome; Individual; Lead; Link; Logic; Lymphocyte; Lymphocyte antigen; Modeling; Molecular; Molecular Conformation; Monitor; Mus; Mutation; Physiological; Play; Receptor Gene; Regulation; Regulator Genes; Regulatory Element; Research; Resolution; Shapes; Site; Spottings; Stretching; Structure; T Chain; T cell differentiation; T-Cell Development; T-Cell Receptor; T-Lymphocyte; Testing; Thymocyte Development; Time; Tissues; Transcriptional Activation; Variant; base; cell type; chromatin modification; cohesin; comparative; driving force; genome-wide analysis; human disease; in vivo; infancy; insight; interest; mammalian genome; novel; novel therapeutics; physiologic model; programs; promoter; three dimensional structure; transcription factor

ABSTRACT Gene expression relies on interplay among cis elements, chromatin domains, and genome architecture. The latter is of intense interest as ~10% of human diseases may arise from defects in genome topology that impact gene expression. Genomes divide into conserved, Mb-sized topologically associated domains (TADs) that are further subdivided into cell type-specific loops between promoter and enhancers (regulatory loops) or between CTCF binding elements (structural loops). In addition, chromatin architecture can be shaped by tissue-specific boundary elements (BEs) that divide active and inactive regions of transcription. These two types of domains tend to associate spatially, perhaps through homotypic chromatin interactions. Foundational questions remain about mechanisms of genome architecture reorganization and its impact on gene expression during cellular differentiation. Answers to these questions have important implications because disease-associated variants in the human genome can disrupt CTCF sites or BEs, enabling aberrant communication between enhancers and alternative promoters that normally partition into separate architectural domains. The co-PIs have approached relationships between genome topology and gene regulation by focusing on the mouse Tcrb antigen receptor locus for several reasons, including: (i) it is a physiological model of manageable complexity (ii) its architecture and transcription are dynamically regulated during T cell development, (iii) it divides into alternating chromatin domains, (iv) changes in topology and transcription are critical for Tcrb assembly by long-range recombination, and (v) its recombination center (RC) has a simple regulatory landscape with one enhancer that communicates with two promoters to initiate all aspects of Tcrb assembly. The PIs' recent collaborations have provided important clues into the dynamics of Tcrb structure at a low level of resolution, but insights into mechanisms that sculpt the observed architectural changes are still lacking. These and other data support their hypothesis that developmental switches between inactive and active Tcrb conformations are orchestrated by tissue- and stage-specific changes in the binding of CTCF to cornerstone elements and by the transcription status of individual gene segments, which cooperate to compartmentalize Tcrb into distinct structural domains and drive homotypic interactions that facilitate long-range Tcrb gene assembly. To test foundational aspects of their hypothesis, the PIs propose to elucidate detailed topologies of active versus inactive Tcrb loci (Aim 1), assess whether transcription status and homotypic chromatin interactions shape Tcrb conformations (Aim 2), and determine mechanisms by which CTCF elements direct Tcrb topology (Aim 3). The co-PIs will monitor multiple physiological readouts (topology, transcription, chromatin, and recombination) to gain unprecedented insights into mechanistic relationships among genome architecture, gene expression, DNA recombination, and factors that sculpt primary lymphocyte antigen receptor gene repertoires

摘要 基因表达依赖于顺式元件、染色质结构域和基因组结构之间的相互作用。这个 后者引起了人们的强烈兴趣，因为大约10%的人类疾病可能是由影响 基因表达。基因组分为保守的、Mb大小的拓扑相关结构域(TADS)，这些结构域 进一步细分为启动子和增强子之间的特定细胞类型的环(调控环)或 CTCF结合元件(结构环)。此外，染色质的结构可以由组织特异性来塑造 划分转录活性区域和非活性区域的边界元件(BE)。这两类域 倾向于在空间上关联，可能是通过同型染色质相互作用。基础性问题依然存在 细胞基因组结构重组的机制及其对基因表达的影响 差异化。这些问题的答案具有重要的意义，因为 人类基因组可以破坏CTCF位点或BES，使增强子和BES之间的异常通信成为可能 通常划分为单独的架构域的备选推动者。协理私隐专员已与 以小鼠Tcrb抗原受体为研究对象的基因组拓扑与基因调控的关系 几个原因，包括：(一)它是一个可管理复杂性的生理模型(二)它的架构 和转录是在T细胞发育过程中动态调节的，(Iii)它分为交替的染色质 结构域，(Iv)拓扑和转录的变化对于通过长距离重组组装Tcrb至关重要， 以及(V)它的重组中心(RC)有一个简单的监管环境，只有一个增强子进行沟通 用两个启动子启动TCRB组装的所有方面。私家侦探最近的合作提供了 对低分辨率的TCRB结构动力学的重要线索，但对机制的洞察 对观察到的建筑变化进行雕刻的方法仍然缺乏。这些数据和其他数据支持他们的假设 不活跃和活跃的Tcrb构象之间的发育切换是由组织和 CTCF与基石元件结合的阶段特异性变化以及转录状态的影响 单独的基因片段，它们协同将Tcrb划分为不同的结构域并驱动 促进远距离Tcrb基因组装的同型相互作用。测试其基础方面 假设，PI建议阐明活动和非活动TCRB基因座的详细拓扑(目标1)，评估 转录状态和同型染色质相互作用是否影响Tcrb构象(目标2)，以及 确定CTCF元素指导TCRB拓扑的机制(目标3)。协管员将监控多个 生理学读数(拓扑、转录、染色质和重组)以获得前所未有的洞察力 基因组结构、基因表达、DNA重组和因子之间的机制关系 塑造初级淋巴细胞抗原受体基因库