p53 Dynamically Directs TFIID Assembly on Target Gene Promoters

ABSTRACT

p53 is a central regulator that turns on vast gene networks to maintain cellular integrity in the presence of various stimuli. p53 activates transcription initiation in part by aiding recruitment of TFIID to the promoter. However, the precise means by which p53 dynamically interacts with TFIID to facilitate assembly on target gene promoters remains elusive. To address this key issue, we have undertaken an integrated approach involving single-molecule fluorescence microscopy, single-particle cryo-electron microscopy, and biochemistry. Our real-time single-molecule imaging data demonstrate that TFIID alone binds poorly to native p53 target promoters. p53 unlocks TFIID's ability to bind DNA by stabilizing TFIID contacts with both the core promoter and a region within p53's response element. Analysis of single-molecule dissociation kinetics reveals that TFIID interacts with promoters via transient and prolonged DNA binding modes that are each regulated by p53. Importantly, our structural work reveals that TFIID's conversion to a rearranged DNA binding conformation is enhanced in the presence of DNA and p53. Notably, TFIID's interaction with DNA induces p53 to rapidly dissociate, which likely leads to additional rounds of p53-mediated recruitment of other basal factors. Collectively, these findings indicate that p53 dynamically escorts and loads TFIID onto its target promoters.

KEYWORDS:

• p53
• TFIID
• transcription
• structure
• single-molecule microscopy

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Supplemental material for this article may be found at https://doi.org/10.1128/MCB.00085-17.

ACKNOWLEDGMENTS

We specifically thank R. Tjian, S. Chu, and E. Nogales for their initial support of this study, S. Zheng for generating TAF4 MAb supernatant and HeLa cells, D. King for providing the TAF4 MAb elution peptide, A. Revyakin, A. Pertsinidis, and S. R. Park for their help on initial stages of the single-molecule microscopy, and R. Henderson for his technical advice critical for the cryo-EM work. We also thank S. M. Shenoy, J. Hargitai, J. Wang, S. Lenny, J. Greally, and E. Eng for high-performance computing cluster and cryo-EM technical support. We appreciate assistance from Einstein's AIF facility, especially F. P. Macaluso, L. Cummins, and G. S. Perumal. We are grateful to M. Keogh, Charles Kenworthy, and E. Nogales for critical comments of the manuscript.

This study was supported by startup funds (Albert Einstein College of Medicine) and by NIH/NIBIB 5U01EB021236-02 (R.A.C.). Some of this work was performed at the Simons Electron Microscopy Center at the New York Structural Biology Center, which is supported by a grant from the Simons Foundation (grant no. 349247) with additional support from NIH S10 OD019994-01, the Agouron Institute (grant no. F00316), NIH S10 RR029300-01, NIH S10 RR017291-01, NYSTAR, and NIH C06 RR017528-01-CEM. The Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, is supported by NIH NIGMS P41-GM103311. W.L.L. is an affiliated member of the New York Structural Biology Center. M.C. is an HHMI fellow of the Damon Runyon Cancer Research Foundation.