| The traditional roles of the tumor suppressor protein, p53, in transcriptional regulation are mostly defined in cancer or stressed cells and are centered on control of the cell cycle, DNA repair or senescence. In this thesis, data is presented demonstrating that the p53-regulated transcriptome is highly context-dependent as illustrated using the developing kidney as a model system. To this end, we utilized whole genome transcriptome and ChIP-Seq (chromatin immunoprecipitation-high throughput sequencing) analyses in p53 +/+ and p53-/- mice to identify p53 regulated pathways in the embryonic kidney. This integrated approach allowed identification of novel genes that are direct p53 targets in the developing nephron. This approach was further refined using RNA-Seq analysis of lineage-tagged FACS-isolated nephron progenitors. We find that the p53-regulated transcriptome in the embryonic kidney is mostly involved in development, morphogenesis, and metabolic pathways. Interestingly, traditional targets of p53, such as DNA repair, cell cycle and apoptosis, accounted for < 5% of differentially expressed genes. The majority of 7,893 p53-binding genomic regions contain consensus p53 binding sites. Unlike a cancer cell line in which 7% of p53 binding sites lie within proximal promoters, 78% of p53 peaks in the developing kidney overlies the promoter. Moreover, 25% of the differentially expressed p53-bound genes belong to nephron progenitors and nascent nephrons, including key transcriptional regulators, components of Fgf, Wnt, Bmp, and Notch pathways, and ciliogenesis genes. RNA-Seq of nephron progenitors from wild-type and mutant p53 mice demonstrated repression of the nephron stem cell marker, Cited1, but not Six2. Moreover, cytoskeleton, cell adhesion, and energy metabolism genes were downregulated in mutant progenitors consistent with the loosely organized cap mesenchyme and disrupted mesenchyme-to-epithelium transition of p53-/- progenitors. In conclusion, our studies demonstrate that p53 genomic occupancy and regulated transcriptome are distinctly different in development and cancer. p53 is a key regulator of transcriptional programs that maintain nephron niche integrity, nephron progenitor cell renewal and differentiation. |
