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

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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