1. Charting the structure of the mammalian genome
Our knowledge of chromatin structure and long-range genomic interactions in mammalian cells is still rudimentary. How do the genomes of lymphocytes, plasma cells and granulocytes adopt such unique and distinct structures? We aim to resolve these questions using genome-wide chromosome-conformation capture studies (HiC) in conjunction with computational approaches to describe the topologies of lymphoid and myeloid genomes in molecular terms.
2. In vivo imaging of long-range genomic interactions
During developmental progression of lymphoid cells coding and regulatory elements interact to induce lineage-specific programs of gene expression. We recently found that in eukaryotic cells coding and regulatory genomic elements bounce back and forth within the chromatin network until specific genomic interactions are established, and that spatial confinement of topological domains largely controls the times for such encounters. Our future studies aim to examine how epigenetic and structural determinants affect the trajectories adopted by the chromatin fiber in living cells and how this relates to genomic encounters involving enhancers and promoters.
3. Live cell imaging to describe pattern of gene transcription and translation
Among the major challenges in immune cell development and physiology is to determine how interactions among molecules give rise to emergent behaviors like lineage specification and commitment, positive selection and negative selection, effector and memory function. We are using and/or plan to use live cell imaging methods to describe the initiation of gene expression, transcriptional elongation, mRNA localization, mRNA export and translation in quantitative terms to address these questions in cells that comprise the immune system.