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

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. Overall design: HCT116-3(6) cells were transiently transfected with lacZ siRNA or p53/p73 siRNA oligo and were then treated with or without HU for 16 hrs. Four biological repeats were performed for each condition (-HU or +HU), with two technical repeats (dye swap) per biological sample.