Enhancer Driven Gene Regulation During Lymphocyte Development

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DESCRIPTION: Lymphoid neoplasms (leukemias and lymphomas) are among the most common malignancies in humans, particularly children. Although they arise from diverse etiologies, the majority are linked to alterations in expression of oncogenes, tumor suppressors and / or transcription factors that are important for lineage specification. In order to identify te underlying cause of the various forms of these cancers it is important to understand the mechanisms underlying the different cellular processes that regulate gene expression in normal cells. We have focused our efforts on one particular aspect of gene regulation that remains poorly understood: enhancer mediated gene regulatory networks. Identifying the enhancer-mediated gene regulatory networks that underpin differentiation remains a challenge because it has been difficult to define the targets of enhancers. Indeed, individual enhancers can in some instances control multiple genes that are not necessarily located in close physical proximity in cis. Some studies have tried to address this using chromosome conformation capture to identify interactions between enhancers and promoters. However, it is not clear whether interactions are predictive of functional regulation so these approaches do not definitively determine the regulatory targets of individual enhancers and the extent to which they contribute to gene expression. To examine the effect of individual enhancers it is necessary to mutate these elements and characterize changes in interactions coupled with gene activity and binding of transcription factors. In this application we aim to perform a series of genome wide analyses to examine these aspects of control using mice that harbor deletions of enhancers associated with immunoglobulin and T cell receptor loci. The data from experiments we have performed to date support a model in which each enhancer participates in transcription by physically relocating each locus into specific sites, perturbation of which (e.g. by deleting a specific enhancer) can have extensive consequences on many loci (both in cis and in trans) that are expressed or repressed at the same site. Based on these findings and data from our lab and others showing that co-regulated genes come together in the nucleus, we hypothesize that the binding of transcription factors or regulators induces a distinct pattern of cell type, stage specific interactions, which form a network that contributes to the control of gene expression. In this application we aim to explore this further and test the limitations of our model by addressing the following questions: (1) What are the mechanisms underlying enhancer-mediated gene regulatory networks? (2) What is the contribution of RAG in controlling antigen receptor enhancer mediated networks? Can we genetically manipulate E? and observe changes in the enhancer mediated regulatory network? Overall the work we propose here will break new ground in our understanding of cell type-specific gene networks and the implications of coordinate locus expression during lymphoid development in cells undergoing normal and aberrant DNA recombination events.