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 ?broblast (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 con?nement, 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 de?ning the contraction process and identify critical genomic interactions. Our speci?c 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 ?rst develop a spatially con?ned random self-avoiding polymer model to exclude non-speci?c 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
We will develop computational methods that can generate ensembles of 3D structures of the Igh locus in B-cells. Our project will provide overall structural understanding of the spatial organization of the Igh locus. It will also identify critical 3D genomic interactions and specify structural features de?ning the contraction process essential for generating antigen receptor diversity. 4
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| Wang, Boshen; Perez-Rathke, Alan; Li, Renhao et al. (2018) A General Method for Predicting Amino Acid Residues Experiencing Hydrogen Exchange. IEEE EMBS Int Conf Biomed Health Inform 2018:341-344 |
| Gürsoy, Gamze; Xu, Yun; Liang, Jie (2017) Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model. PLoS Comput Biol 13:e1005658 |
| Gürsoy, Gamze; Xu, Yun; Kenter, Amy L et al. (2017) Computational construction of 3D chromatin ensembles and prediction of functional interactions of alpha-globin locus from 5C data. Nucleic Acids Res 45:11547-11558 |
