Estimation of a Genome’s Spatial Organization from Gene Expression Data of Cell Subpopulations
Cells sense biochemical signals from their local microenvironment and transduce them to the nucleus to regulate gene expression programs. Interestingly, the same cell with different spatial organization states can elicit distinct expression patterns when subjected to the same biochemical signal. Despite an explosion in ways to probe a cell’s genome and its environment, the general principle of how spatial organization and gene expression are linked remains unknown. In this study, we aim to explain the heterogeneity observed in CD4+ T cell gene expression by the variation in spatial organization. Using known spatial organization and gene expression states of naive and activated CD4+ T cells we explore the function that links spatial organization to gene expression. For novel T cell subpopulations, where spatial organization is unknown, we aim to develop a predictive model that infers spatial organization using gene expression as input and thus allows us to develop a better understanding of gene regulation in a particular cell type.
Authors: Anastasiya Belyaeva
