SUMMARY
Tumor-suppressor p53 regulates transcription of stress response genes. Many p53 targets remain undiscovered due to uncertainty as to where p53 binds in the genome, and that few genes reside near p53-bound recognition elements (REs). Using ChIP-exo, we associated p53 with 2,183 unsplit REs. REs were positionally constrained with other REs and other regulatory elements, which may reflect structurally organized p53 interactions. Surprisingly, stress resulted in increased occupancy of TFIIB and RNA polymerase (Pol) II near REs, which was reduced when p53 was present. A subset associated with antisense RNA near stress-response genes. The combination of high-confidence locations for p53/REs, TFIIB/Pol II, and their changes in response to stress allowed us to identify 151 high-confidence p53-regulated genes, substantially increasing the number of p53 targets. These genes comprised a large portion of a pre-defined DNA-damage stress-response network. Thus, p53 plays a comprehensive role in regulating the stress-response network, including regulating noncoding transcription.