Nucleosomes gate cofactor access to the transcription factor p53 [ChIP-seq]

The transcription factor p53 regulates cell cycle progression, apoptosis, and the DNA damage response. A large fraction of p53 resides in inaccessible chromatin, where it is unclear how nucleosomes impact p53's ability to engage cofactors. We examined the interaction of p53 with the members of the ubiquitin proteasome system (UPS) on chromatin. At two distinct motif locations (SHL-5.7, +5.9), the viral E3 ubiquitin ligase E6-E6AP was unable to bind nucleosome-engaged p53. The deubiquitinase USP7, on the other hand, readily engages nucleosome-bound p53 in vitro and in cells. The corresponding cryo-EM structure finds USP7 intricately engaged with p53 and nucleosomes, with the TRAF domain contacting the nucleosome at SHL-5.7 sandwiched between the p53 tetramerisation and DNA-binding domains. The structures of p53 bound to USP7/nucleosomes and E6AP illustrate how chromatin imposes a barrier for some, albeit not all p53 interactors. Our work suggests a conceptual framework for how nucleosomes govern TF/cofactor interactions. Overall design: Examination of p53 and USP7 in mouse embryonic stem cells. Includes Usp7 ChIPseq in mouse ESC lines under p53untreated/p53-activated conditions (duplicates), IgG control ChIPseq in wildtype mouse ESC lines (duplicates). Conditions to activate p53 performed for 4 hours.