Constructing Ensembles of 3D Structures of Igh Locus and Predicting Novel Chromosomal Interactions

项目摘要/摘要 免疫生物学的一个中心问题是了解获得性免疫反应。缩水 免疫球蛋白重链(IgH)基因座的处理是后续VDJ加入事件的关键 以产生抗原受体多样性。为了从机械上理解这一收缩过程， 我们建议开发新的计算方法来研究IGH轨迹的空间结构 在收缩之后。我们将生成详细的3D结构集成的染色质链 基于从染色体构象捕获碳拷贝获得的环相互作用的基因座 (5)小鼠胚胎成纤维细胞(fi)和原代PRO-B(PRO-B)淋巴细胞的研究。 这些染色质链的3D模型将满足自回避的基本聚合物特性 和核连接，将解释来自5C研究的相互作用，并可以代表 免疫球蛋白基因座的群体和可能的异质性亚群。此外，我们还将指定 收缩过程中的结构特征defi并确定关键的基因组相互作用。 我们的特殊fic目标是(1)开发一种计算方法来生成大型系综。 1056个代表细胞群体和亚群的IgH基因座的3D染色质链 基因座收缩前后的种群数量。我们将首先开发一个空间连续的fifiNed随机数 自回避聚合物模型，从5C测量中排除非特定fic 3D环路相互作用。 然后我们将开发一种方法来生成满足5C-派生的大型染色质链集合 可以代表细胞群体和亚群体的相互作用。然后我们将(2)指定 基因重组前后基因组元件的共性和差异性的三维相互作用模式 牵引，并通过计算基因敲除研究确定关键的3D基因组相互作用。这个 我们的工作成果将是IGH轨迹空间组织的详细结构图 以及一组用于构建3D染色质结构的强大计算工具 这可以应用于任何基因组位置。 3.

Project Summary/Abstract A central problem of immunobiology is to understand the adaptive immune response. The contraction process of the immunoglobulin heavy chain (Igh) locus is essential for subsequent VDJ joining event to generate antigen receptor diversity. To gain mechanistic understanding of this contraction process, we propose to develop novel computational methods to study spatial structures of the Igh locus before and after contraction. We will generate detailed 3D structural ensembles of chromatin chains of the locus based on looping interactions obtained from chromosome conformation capture carbon copy (5C) studies of the mouse embryonic fibroblast (MEF) cells and the primary pro-B (pro-B) lymphocytes. These 3D models of chromatin chains will satisfy fundamental polymer properties of self-avoidance and nuclear confinement, will account for interactions derived from 5C studies, and can represent the population and possible heterogeneous subpopulations of the Igh locus. In addition, we will specify structural features defining the contraction process and identify critical genomic interactions. Our specific aims are to (1) develop a computational method to generate large ensembles of 1056 3D chromatin chains of the Igh locus representative of cell populations and sub- populations before and after the locus contraction. We will first develop a spatially confined random self-avoiding polymer model to exclude non-specific 3D looping interactions from 5C measurements. We will then develop a method to generate large ensembles of chromatin chains satisfying 5C-derived interactions that can represent the population and sub-populations of cells. We will then (2) specify common as well as differential 3D interaction patterns of genomic elements before and after con- traction, and identify critical 3D genomic interactions through computational knock-out studies. The outcome of our work will be a detailed structural picture of the spatial organization of the Igh locus during contraction, as well as a set of powerful computational tools for building 3D chromatin structures that can be applied to any genomic locus. 3