Epigenetic mechanisms of gene regulation in nephron progenitor cell proliferation and differentiation

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The long-term goal of the proposed work is to determine mechanisms that control gene regulatory networks to generate a normal endowment of mature nephrons. Formation of the proper complement of nephrons requires a balance between self-renewal and differentiation of progenitor cells. Disruption of this balance leads to renal hypoplasia and chronic kidney disease. Soon after progenitor cells begin to differentiate, chromatin must undergo significant changes to set up gene expression patterns for formation of distinct cell types along the nephron. Defects in formation of specific renal epithelial cell types leads to glomerular disease and an inability of tubules to perform normal physiological functions, such as maintaining salt and water balance. A major mechanism by which cells respond to signals to direct gene expression to a particular fate or lineage is through the concerted action of chromatin remodeling complexes and tissue restricted transcription factors. These proteins act on regulatory regions in the genome to establish control of gene expression at the correct time and place. While individual factors that control gene expression in nephron progenitor cells have been defined, how these proteins cooperate to control gene expression in the developing kidney has not been explored. The identification and characterization of the regulatory elements where these factors act is also a major challenge in the field. We discovered that Sall1 plays a pivotal role in these developmental decisions by interacting with two distinct chromatin remodeling complexes, the Nucleosome Remodeling and Deacetylase (NuRD) complex and the Switch/Sucrose Non-Fermentable (SWI/SNF) complex. We propose that the integrated actions of Sall1, Six2, NuRD and SWI/SNF controls nephron progenitor cell gene expression to attain a dynamic balance between self-renewal and differentiation, and establishes the epigenetic modifications required for formation of specific cell lineages in the mature kidney. This novel paradigm will be tested in three Aims. In Aim 1, we will perform Hi-ChIP to identify enhancer-promoter contacts in uncommitted and induced progenitors, and define changes in mutant cells. Aim 2 will determine how genomic binding of Sall1, Six2, NuRD and SWI/SNF are affected in mutant nephron progenitor cells. Epigenomic editing will be used to demonstrate causal relationships between gene expression and binding of these factors at regulatory regions. In order to translate our findings to human development and disease, in Aim 3 we will test our findings in the mouse from Aims 1 and 2 in human iPS cell-derived nephron progenitor cells. These studies will illuminate mechanisms that underlie human genetic syndromes and sporadic birth defects, such as renal hypoplasia, which commonly cause childhood kidney failure. Our findings will also provide insight into how to reprogram kidney cells from a differentiated state back to a progenitor state, to promote regeneration of mature tubular epithelial cells in order to correct nephron deficits.