The 3D-Structure of the Immunoglobulin Heavy Chain Locus

免疫球蛋白重链基因座的 3D 结构

• 批准号: 8082190
• 负责人: CORNELIS MURRE
• 金额: $ 14.63万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-09 至 2011-08-08
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8082190
• 关键词: Adopted; Antibody Diversity; Antibody Repertoire; Antigen Receptors; B-Cell Development; B-Lymphocytes; Biological; Biological Models; Cell Lineage; Chromatin; Chromatin Fiber; Chromatin Structure; Code; Computer Simulation; Data; Development; Elements; Family; Fiber; Frequencies; Generations; Genetic; Genome; Genomics; Goals; Heavy-Chain Immunoglobulins; Higher Order Chromatin Structure; IGH@ gene cluster; Immune response; Interphase; Invaded; Lighting; Measurement; Microscopic; Microscopy; Mitotic; Mitotic Chromosome; Molecular; Molecular Conformation; Positioning Attribute; Property; Receptor Gene; Relative (related person); Research; Resolution; Simulate; Spatial Distribution; Structure; base; insight; mammalian genome; pathogen; public health relevance; telomere; three dimensional structure

DESCRIPTION (provided by applicant): The long-range goals of the research proposed in this application are to determine at high resolution the 3D-structure of the immunoglobulin heavy chain (Igh) locus. The Igh locus is organized into distinct regions that contain multiple variable (VH), diversity (DH), joining (JH) and constant (CH) coding elements. To probe the topography of the Igh locus, we have recently determined the spatial distance distributions using 12 genomic markers that spanned the entire locus. These spatial distance distributions were compared to computer simulations of alternative chromatin arrangements. This analysis predicted that the Igh locus is organized into compartments containing clusters of loops separated by linkers. We then used computational geometry to determine the mean relative 3D-positions of the VH, DH, JH and CH elements. Briefly, the data showed that during early B cell development, the entire repertoire of VH regions (2.5 Mbp) is merged and juxtaposed to the DH elements, allowing the VH regions to encounter DHJH elements with relatively high and similar frequencies. Here we propose to continue these studies. We would describe at high resolution the average Igh locus trajectories in interphase and mitotic chromatin. We would determine the spectrum of conformations adopted by the Igh locus fiber. We would use structured illumination microscopy to visualize the Igh chromatin territories. We would characterize compartments using physical approaches. We would identify loop bases using both physical and molecular biological approaches. We would use spatial distance measurements and computational geometry to determine whether the Igh locus structure is a general feature of antigen receptor loci and eukaryotic interphase chromatin. Taken together, these studies would provide a statistical description of Igh locus structure and provide mechanistic insight into how antibody diversity is generated. PUBLIC HEALTH RELEVANCE: In previous studies we have used geometry to show how a genetic locus is organized in 3D space. The studies proposed in this application should provide insight into how the structure of the genome permits the generation of an immune response to a wide variety of invading pathogens.

描述(由申请人提供)：本申请中提出的研究的长期目标是以高分辨率确定免疫球蛋白重链(IgH)基因座的三维结构。IgH基因座被组织成包含多个可变(VH)、多样性(Dh)、连接(JH)和恒定(CH)编码元件的不同区域。为了探索IgH基因座的地形，我们最近使用了横跨整个基因座的12个基因组标记来确定空间距离分布。将这些空间距离分布与可选染色质排列的计算机模拟进行比较。这一分析预测，IgH基因被组织成包含由连接子分隔的环簇的隔间。然后，我们使用计算几何来确定VH、DH、JH和CH元素的平均相对3D位置。简而言之，数据表明，在B细胞发育的早期，VH区的整个谱系(2.5Mbp)被合并并并列到DH元件，使VH区能够遇到频率相对较高和相似的DHJH元件。在这里，我们建议继续进行这些研究。我们将在高分辨率下描述间期和有丝分裂染色质的平均IgH轨迹。我们将确定IGH轨迹纤维所采用的构象光谱。我们将使用结构照明显微镜来显示IGH染色质区域。我们将使用物理方法来描述隔间的特征。我们将使用物理和分子生物学方法来鉴定环碱基。我们将使用空间距离测量和计算几何来确定IgH基因座结构是否是抗原受体基因座和真核细胞间期染色质的一般特征。综上所述，这些研究将提供对IgH基因座结构的统计描述，并提供对抗体多样性如何产生的机械性洞察。与公共健康相关：在之前的研究中，我们已经使用几何学来展示遗传位点是如何在3D空间中组织的。这项申请中提出的研究应该有助于深入了解基因组的结构如何允许对各种入侵病原体产生免疫反应。