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Gene expression profiling in p53 and p73 double knockdown HCT116-3(6) cells

ABSTRACT: The main goal of this study is to integrate gene expression analysis with ChIP-chip study. To examine the relationship between promoter occupancy and gene expression, we transiently depleted p53 and p73 via small interfering RNA (siRNA) in HCT116-3(6) cells and then performed microarray analysis of 32,000 genes before or after HU treatment using the Phalanx expression array platform. We found that only 6%-14% of p53 and p73 bound promoters at FDRMAP <0.05 exhibited significant changes in mRNA expression when p53 and p73 were simultaneously knocked-down by siRNA. The minimal correlation between binding and regulation of expression is consistent with previous observations of the lack of transcriptional effects at many transcription factor binding sites.

ORGANISM(S): Homo sapiens

PROVIDER: GSE12242 | GEO | 2009/06/30

SECONDARY ACCESSION(S): PRJNA113705

REPOSITORIES: GEO

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p53 and p73 ChIP-chip experiments in HCT116-3(6) cells

Project description:The p53-family of transcription factors share a highly homologous DNA binding domain and have overlapping and distinct biological functions. Using chromatin immunoprecipitation in combination with NimbleGen promoter arrays and a Model-based Algorithm for Promoter arrays (MAP), we performed a direct comparison of the promoter occupancy profiles of p53 and p73 before and after treatment with hydroxyurea (HU). We have found that p53 and p73 bind to common promoters before HU treatment. After HU treatment, we found that p53-bound promoters are likely to also bind p73, but p73 binds to additional promoters that that do not bind p53. Among them, we showed that p73 but not p53 is recruited to the promoter of MLH3, which encodes a mismatch repair protein. The differential effects of HU on the promoter occupancy profiles of p53 and p73 suggest that these related transcription factors have divergent functions in DNA damage response. The main goal of this study is to examine the effect of HU on the promoter occupancy profiles of p53 and p73. One biological sample from HCT116-(6) cells treated with or without Hydroxyurea was subjected to ChIP-chip analysis using a model based algorithm for promoter arrays (MAP).

2009-06-30 | E-GEOD-12224 | biostudies-arrayexpress

p53 and p73 ChIP-chip experiments in HCT116-3(6) cells

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