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

项目总结/摘要 免疫生物学的一个中心问题是理解适应性免疫反应。收缩 免疫球蛋白重链（Igh）基因座的过程对随后的VDJ连接事件至关重要 来产生抗原受体多样性。为了获得对这种收缩过程的机械理解， 我们建议开发新的计算方法来研究Igh基因座的空间结构， 收缩后。我们将生成详细的3D结构合奏的染色质链的 基于从染色体构象捕获碳拷贝获得的成环相互作用的基因座 (5C)小鼠胚胎成纤维细胞（MEF）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 和核确认，将解释来自5C研究的相互作用，并可以代表 群体和Igh基因座的可能异质亚群。此外，我们将指定 定义收缩过程的结构特征，并确定关键的基因组相互作用。 我们的具体目标是（1）开发一种计算方法来生成大型合奏 的1056个3D染色质链的Igh基因座代表细胞群体和亚细胞， 在轨迹收缩之前和之后的群体。我们将首先开发一个空间受限的随机 自避免聚合物模型，以从5C测量中排除非特异性3D循环相互作用。 然后，我们将开发一种方法来产生满足5C衍生的染色质链的大集合。 可以代表细胞的群体和亚群体的相互作用。然后我们将（2）指定 共同以及差异的三维相互作用模式的基因组元件之前和之后， 牵引，并通过计算敲除研究确定关键的3D基因组相互作用。的 我们的工作成果将是一个详细的结构图片的空间组织的免疫球蛋白基因座 以及一套用于构建3D染色质结构的强大计算工具 可以应用于任何基因组位点。 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