Project description:Study of the function of p53 in regulating gene expression in mouse embryonic stem cells. It is critical for embryonic stem cells to maintain their genomic stability. The guardian of the genome, p53, plays important roles in maintaining the genomic integrity of ES cells through regulating the differentiation of ES cells. However, the underlying mechanism of this differentiation is still unclear. We plan to use the integrative genome-wide approach, combining ChIP-seq and gene expression microarray, to explore the mechanisms. Total six samples: two inputs (untreated and treated with adriamycin) and four ChIP samples (p53_untreated, p53_adr8h, p53S18P_untreated, p53S18P_adr8h). The two inputs will serve as controls for identifying the binding sites.
Project description:The goal is to identify regulatory RNAs that regulate the p53 signaling pathway in embryonic stem (ES) cells. p53+/+ mES cells and p53-/- mES cells were untreated or treated with 0.5 uM Adriamycin for 8 hours. Total RNA was extracted and subject to RNAseq.
Project description:The goal is to profile several histone modifications and hnRNP L in untreated or Adriamycin-treated mouse embryonic stem cells. Fifty million of R1E mES cells were untreated or treated with 0.5 uM Adriamycin for 8 hours. Fixed cells were subject to ChIP-seq assay.
Project description:The tumor suppressor p53 regulates the differentiation of embryonic stem (ES) cells upon DNA damage. However, our understanding of this critical tumor suppressive role of p53 in ES cells is limited, mainly because of the lack of molecular mechanism. Here, we report a widespread cross-regulation of p53-mediated DNA damage signaling and the pluripotent gene network in ES cells using chromatin-immunoprecipitation assay-based sequencing (ChIP-seq) and gene expression microarray. Upon DNA damage, p53 directly regulates the transcription of 3644 genes (p<0.005) in mouse ES cells. Genome-wide analysis revealed a dramatic difference between the regulation of p53-activated and -repressed genes. p53 mainly regulates the promoter regions of activated genes, whereas the main regulatory regions for repressed genes reside in distal regions. Among p53-repressed genes, many are pluripotent transcription factors of ES cells, such as Oct4, Nanog, Sox2, Esrrb, c-Myc, n-Myc and Sall4. Strikingly, these transcriptional factors also directly regulate the transcription of the Trp53 gene, highlighting a previously under-estimated transcriptional regulation of p53 in ES cells. Therefore, p53 signaling and ES pluripotent transcriptional networks form an intertwined circuitry. Together, our results provide mechanistic insights into the crosstalk of p53-mediated DNA damage and ES cell "stemness" transcriptional gene networks and shed light on the tumor suppressive function of p53 in ES cells. The goal of this experiment is to identify the gene expression changes after adriamycin treatment in a p53-dependent manner. Total six samples: triplicates for untreated mES cells and triplicates for mES cells treated with adriamycin.
