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

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. 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.