3D_spatial_genomics

Many diseases originate from progressive changes in cell type-specific transcriptional programs, which are regulated to a large extent by distant cis-regulatory chromatin interactions. Measurements of how these interactions spatially change amid different cell-types within tissues will be critical to understand normal tissue function and the regulatory mechanisms underpinning disease progression. In this project, we propose to use a novel imaging-based technology that we pioneered to monitor transcriptional status and 3D chromatin organization in single-cells with spatial resolution. Specifically, we will apply this technology to investigate how progression of type-2 diabetes impacts transcriptional output and its 3D cis-regulation in different pancreatic islet cell types. First, we will Identify and study tissue- and cell-type specific chromatin topologies to study the role of loop extrusion and of specific enhancer-promoter configurations in cell-type specific gene regulation of mice loci associated with human T2D. Second, we will apply novel spatial bioinformatics methods to investigate enhancer models and the spatial organization of 3D chromatin organization in tissues. Third, we will monitor changes in cell-type specific chromatin organization during metabolic and genetic perturbations to dissect the contribution of loop extrusion and 3D cis-regulatory interactions to the regulation of transcriptional programs leading to defective insulin secretion. Finally, we perform experiments in human islets from healthy and T2D patients to map 3D chromatin structure changes in well-known T2D associated genes. This innovative approach will: provide insight into the mechanism of transcriptional cis-regulation in healthy tissues, enable investigation of disease mechanisms, such as how disease begins and expands from single cell states, and identify cell states that may drive disease risk.