Single-molecule studies reveal that p53 non-specifically samples nucleosomes to form short-lived complexes with its response element

The transcription factor p53 is a tumor suppressor protein that regulates the expression of genes controlling cell fate decisions. Tetrameric p53 binds to DNA sequences known as response elements (RE) to control transcription via interactions with co-regulatory complexes. It is unclear, however, how p53 recognizes and binds to REs that are occluded when DNA is wrapped around histone octamers to form nucleosomes. Here we used in vitro single molecule microscopy to monitor in real time human p53 binding and releasing from free DNA and nucleosomes containing an RE. On free DNA the frequency and rate of p53 association was independent of the RE, while the formation of kinetically stable complexes was RE-dependent. On nucleosomes, stable binding was not observed, only rapid on/off binding. Most interactions were non-sequence specific and lasted a fraction of a second, regardless of the presence or position of the RE. However, a small population of p53/nucleosome complexes required the RE and lasted a few seconds. The size of this population increased as the RE was moved into the linker DNA. Our data suggest p53 transiently and non-specifically samples nucleosomes to find its RE and form short-lived complexes with the potential to activate transcription.