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: 9753111
• 负责人: CRAIG H BASSING
• 金额: $ 72.24万
• 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/9753111
• 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

抽象的 基因表达依赖于顺式元素，染色质结构域和基因组结构之间的相互作用。这 后者具有强烈的兴趣，因为约有10％的人类疾病可能来自影响的基因组拓扑缺陷 基因表达。基因组分为保守的MB大小拓扑相关域（TAD） 进一步细分为启动子和增强子（调节循环）之间的细胞类型特异性环或 CTCF结合元件（结构环）。另外，染色质结构可以通过组织特异性形成 边界元素（BES）将转录的活跃和不活跃区域分开。这两种类型的域 倾向于通过同型染色质相互作用在空间上关联。仍然存在基本问题 关于基因组结构重组的机制及其对细胞过程中基因表达的影响 分化。这些问题的答案具有重要的含义，因为与疾病相关的变体 人类基因组可以破坏CTCF站点或BES，从而使增强剂和 通常将通常分配到单独的建筑领域的替代启动子。共同案件已接近 通过关注小鼠TCRB抗原受体，基因组拓扑与基因调节之间的关系 基因座的原因有几个，包括：（i）它是可管理复杂性的生理模型（ii）其体系结构 在T细胞发育过程中，转录受到动态调节，（iii）将其分为交替的染色质 域，（iv）拓扑和转录的变化对于通过远程重组的TCRB组装至关重要， （v）其重组中心（RC）具有一个简单的调节景观，并具有一个增强器 有两个启动子启动TCRB组装的各个方面。 PI的最近合作提供了 在低水平的分辨率下，重要的线索进入TCRB结构的动力学，但对机制有见识 雕刻观察到的建筑变化仍然缺乏。这些数据和其他数据支持其假设 组织和活性TCRB构象之间的发育切换由组织和 CTCF与基石元素的结合以及通过转录状态的特定阶段特异性变化 单个基因段，合作将TCRB划分为不同的结构域并驱动 促进远程TCRB基因组装的同种异型相互作用。测试他们的基本方面 假设，PI提议阐明主动与非活动性TCRB基因座的详细拓扑（AIM 1），评估 转录状态和同型染色质相互作用是否形成TCRB构象（AIM 2）和 确定CTCF元素直接TCRB拓扑的机制（AIM 3）。 Co-Pis将监视多个 生理读数（拓扑，转录，染色质和重组）以获得前所未有的见解 进入基因组结构，基因表达，DNA重组和因素之间的机械关系 雕刻原代淋巴细胞抗原受体基因曲目