FIGURE 3.

An induced TP53 shRNA regulates fewer transcripts than a corresponding siRNA. HCT-116 cells stably expressing a tetracycline regulatable transcriptional repressor and encoding a TP53 shRNA under control of a doxycycline-inducible promoter were treated with doxycycline. Wild-type HCT116 cells were transfected with an siRNA of the same 19-mer core sequence. In the top panels, RNA was harvested 48 h after induction of RNAi and subjected to microarray analysis. Gene expression signatures (P-value <0.01) were determined and plotted as described above. Down-regulated transcripts are indicated in green, up-regulated transcripts are shown in red, and the target transcript is shown in magenta. Blue indicates no significant change. In the bottom panel, RNA from cells treated with the TP53 siRNA or induced with doxycycline to express the TP53 shRNA was harvested 24 h after treatment. For this experiment, we interrogated all ∼22,000 genes on the Agilent array platform used in the experiment. For the cluster analysis, cuts were set such that only genes regulated by at least one experiment in the cluster are shown.