Constructing High-Resolution Ensemble Models of 3D Single-Cell Chromatin Conformations of eQTL Loci from Integrated Analysis of 4DN-GTEx Data towards Structural Basis of Differential Gene Expression

To enhance the utility of the common fund supported 4D Nucleome (4DN) database and Genotype- Tissue Expression (GTEx) database, we will develop novel computational tools for infering the spatial organizations of genomic elements to elucidate how eQTLs can regulate the expression of their target genes. Our tools will integrate 4DN and GTEx data and overcome the limit of the 2D nature of Hi-C frequency heatmaps, enabling construction of large 3D ensembles of high-resolution models of single-cell chromatin conformations for loci containing tissue-specific genetic variants associated with differential expression. By accounting for 3D polymer effects of random collision between genomic elements due to nuclear volume confinement, our tools will identify chromatin interactions that are statistically significant and likely biologically important. With the ensemble model of single-cell 3D chromatin conformations, our tools will further identify participating genes, promoters, enhancers, and other elements, and elucidate how they are physically arranged in space around genetic variants associated differential gene expression, including how units of higher order many-body interaction for gene regulation may form. In addition, our tools will quantify the presence of heterogeneous subpopulation of cells with different chromatin 3D configurations, allowing probabilistic understanding of the heterogeneous physical interactions around eQTLs. With planned comparative analysis of 3D chromatin conformations from different tissues, different spatial pattern of arrangement of genes and elements important for gene expression will be uncovered, resulting better understanding of genome structure and function relationship. Overall, we will demonstrate significant added-power of integrating two important Common Fund data resources and will provide tools to facilitate understanding the relationship between genome topology and gene expression. Our work will enable highly specific and compelling testable hypothesis on mechanisms of gene regulation to be formulated based on the reconstructed 3D spatial genome topology at loci that harbor variants and eGenes. Validation or refutation of these hypotheses will lead to new insight into the relationship of genome structure and genome function important for improving human health.