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Genome-wide analysis revealed a crosstalk between p53 and the pluripotent gene networks in mouse embryonic stem cells (ChIP-Seq)

ABSTRACT: 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.

ORGANISM(S): Mus musculus

SUBMITTER: Jing Huang

PROVIDER: E-GEOD-26361 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Distinct regulatory mechanisms and functions for p53-activated and p53-repressed DNA damage response genes in embryonic stem cells.

Li Mangmang M He Yunlong Y Dubois Wendy W Wu Xiaolin X Shi Jianxin J Huang Jing J

Molecular cell 20120301 1

p53 is critical in regulating the differentiation of ES and induced pluripotent stem (iPS) cells. Here, we report a whole-genome study of p53-mediated DNA damage signaling in mouse ES cells. Systems analyses reveal that binding of p53 at the promoter region significantly correlates with gene activation but not with repression. Unexpectedly, we identify a regulatory mode for p53-mediated repression through interfering with distal enhancer activity. Importantly, many ES cell-enriched core transcri ...[more]

PMID: 22387025

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Genome-wide analysis revealed a crosstalk between p53 and the pluripotent gene networks in mouse embryonic stem cells (expression)

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.

2012-03-05 | E-GEOD-26360 | biostudies-arrayexpress

Regulatory RNA Apela Is a Component of a Negative Feedback Loop Regulating p53-Mediated Apoptosis in Embryonic Stem Cells (II)

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.

2015-06-05 | E-GEOD-60843 | biostudies-arrayexpress

Genome-wide analysis revealed a crosstalk between p53 and the pluripotent gene networks in mouse embryonic stem cells (ChIP-Seq)

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.

2012-03-05 | GSE26361 | GEO

Regulatory RNA Apela Is a Component of a Negative Feedback Loop Regulating p53-Mediated Apoptosis in Embryonic Stem Cells (III)

Project description:The goal is to identify RNAs that bind to Hnrnpl (hnRNP L) using RNA immunoprecipitation (RIP) assay. p53+/+ mES cells and p53-/- mES cells were untreated or treated with 0.5 uM Adriamycin for 8 hours. RNA immunoprecipitation was performed using Hnrnpl antibody (Bethyl, Cat#: A311-423A). Total RNA was extracted and subject to RNAseq.

2015-06-05 | E-GEOD-62378 | biostudies-arrayexpress

Epigenetic marks and factors binding to chromatin in mouse embryonic stem cells

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.

2015-06-05 | E-GEOD-62864 | biostudies-arrayexpress

The effect on gene expression by p53 family members and the knockdown of AKR1B10

Project description:To evaluate the effect on gene expression by p53 family members and AKR1B10, we overexpressed p53 family members in H1299 cells or knocked down AKR1B10 in HCT116 cells and evaluated the gene expression by microarray analysis. Gene expression was measured in H1299 cells infected with adenovirus expressing p53, p63g and p73b, and in HCT116 cells transfected with siRNAs targeting AKR1B10 and then treated with adriamycin.

2013-10-31 | E-GEOD-47096 | biostudies-arrayexpress

Analysis of MOF under stress conditions

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2015-07-10 | E-GEOD-70706 | biostudies-arrayexpress

p53 coordinates Wnt and TGF-β inputs on mesendoderm differentiation genes

Project description:The TGF-β superfamily member Nodal triggers mesendoderm differentiation in embryonic stem (ES) cells. This transition however requires cooperating Wnt signaling inputs. Here we report that p53, a powerful tumor suppressor in adult tissues, orchestrates this cooperation. We show that p53, which is released from inhibition as mouse ES cells exit from pluripotency, acts as a direct inducer of Wnt3 expression. Wnt-activated Tcf3 then converges with Nodal-activated Smad transcriptional complexes on mesendoderm specification super-enhancers. p53 and its homolog p73 act redundantly in Wnt induction. When p53 and p73 are depleted, the ES cells fail to secrete autocrine Wnt ligands, Tcf and Nodal-activated Smads fail to bind to mesendoderm gene enhancers, and the cells adopt ectoderm rather than mesendoderm identity. Enforced Wnt3 expression or addition of Wnt3a rescues mesendoderm differentiation in p53/p73-depleted ES cells. Thus, independently of their established role as tumor suppressors that guard genome integrity in mature cells, p53 and p73 serve a primordial role in ES cell differentiation by driving a cooperation of Wnt and TGF-β transcriptional inputs on mesendoderm identity gene enhancers.

2017-01-06 | GSE70486 | GEO

Whole-genome study reveals distinct mechanisms used by p53 to regulate activated and repressed genes in embryonic stem cells

Project description:This SuperSeries is composed of the following subset Series: GSE26360: Genome-wide analysis revealed a crosstalk between p53 and the pluripotent gene networks in mouse embryonic stem cells (expression) GSE26361: Genome-wide analysis revealed a crosstalk between p53 and the pluripotent gene networks in mouse embryonic stem cells (ChIP-Seq) Refer to individual Series

2012-03-05 | E-GEOD-26362 | biostudies-arrayexpress

Genome-wide analysis revealed a crosstalk between p53 and the pluripotent gene networks in mouse embryonic stem cells (expression)

2012-03-05 | GSE26360 | GEO