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.

4. Novel strategies to study immune cell differentiation, selection and activation

We are using cutting edge approaches to bridge the gap between studies of individual molecules, gene regulatory elements such as enhancers, insulators and promoters, mRNA and proteins versus collections of molecules. We are using multi-scale approaches that we integrate across spatial and temporal scales to understand how interactions among these factors combine to determine the physiology of the cell. Currently we are focusing on introducing these new approaches to the study of molecular and physical mechanisms that underpin hematopoiesis in young and aging organisms. We are interested in addressing these problem using single-cell imaging but in the context of live tissue such as the thymus and lymph node.

5. Dissecting the roles of large intergenic RNAs in early B cell development

Recent genome-wide studies have identified that a large fraction of the genome transcribed in non-coding regions.  We are now faced with the question as to how these large non-coding RNAs relate to the control of gene expression. We have identified a subset of lineage-specific and developmental-stage specific non-coding RNAs.  Our interests are to determine the function of these non-coding RNAs and to study their potential roles in modulating long-range chromatin structure and genomic interactions.