During fiscal year of 2012, we have made significant progress of mapping genome-wide p53 signaling in embryonic stem cells. 1) It is known that p53 is a potent differentiation inducer of ES cells. However, the mechanisms of how p53 regulates the differentiation of ES cells are not fully appreciated. Some studies including ours suggest that p53 induces differentiation by repressing the transcription of ES-enriched genes, such as Nanog, a master regulator of ES cells. However, Nanog is not strictly required for the maintenance of ES cells, suggesting other mechanisms exist. To explore these other mechanisms, we introduced the powerful ChIP-seq technology into our study. Using this technology, we surprisingly found that p53 not only down-regulates ES-enriched genes but also up-regulates differentiation-associated genes. 2) In addition, p53 regulates the expression of ES-enriched genes and differentiation-associated genes using different mechanisms. For differentiation-associated genes, p53 tend to up-regulate their expression through acting in the promoter region. For ES-enriched genes, p53 generally binds to the distal enhancers and interferes with their activity. In addition to studying p53 signaling in ES cells at a genome-wide level, we also investigate this at a single-transcript level. We recently identified a ES-specific p53 target, the hairless (Hr) gene. The Hr protein contains a JmjC domain, which is a histone demethylation domain. Knocking down of Hr decreases p53-mediated apoptosis in ES cells, suggesting that Hr participates in p53 gene network in ES cells. Earlier work by others have shown that Hr may have a role in lymphomagenesis. Our currently study focuses on investigating the mechanism by which Hr regulates p53-mediated apoptosis in ES cells. This study will shed light on the epigenetic regulation of p53 signaling in ES cells as well in cancer. Only 2 percentage of the genome expresses protein-coding genes. The rest of the genome actively expresses non-coding RNAs, which play important roles in various biological processes. However, the roles of these non-coding RNAs in ES cells are largely unexplored. Using genome-wide approaches, we have identified several non-coding RNAs that may be involved in p53 signaling in ES cells. We are currently studying the roles of these non-coding RNAs in ES cells. Some of these non-coding RNAs bind to chromatin binding protein. In light of these new observations, we define transcripts as protein-coding and non-coding RNAs. 3) Human ES cells are a better model than mouse ES cells. In the fiscal year 2012, we have obtained two human ES cell lines from the Stem Cell Facility at the University of Connecticut. These two human ES cell lines are approved human ES cell lines that can be studied using federal funding. We will use study p53 signaling in human ES cells using these two human ES cell lines. Then, we will compared p53 signaling in mouse ES cells to that in human ES cells with the hope to derived conserved p53 gene network.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
1ZIABC011158-04
Application #
8553009
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
4
Fiscal Year
2012
Total Cost
$901,143
Indirect Cost
Name
National Cancer Institute Division of Basic Sciences
Department
Type
DUNS #
City
State
Country
Zip Code
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Shi, Jianxin; Marconett, Crystal N; Duan, Jubao et al. (2014) Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nat Commun 5:3365
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