A Comprehensive and High-Resolution Genome-wide Response of p53 to Stress

Chang, Gue Su; Chen, Xiangyun Amy; Park, Bong Soo; Rhee, Hyun‐Ku; Li, Pingxin; Han, Kang Hoo; Mishra, Tejaswini; Chan-Salis, Ka Yim; Li, Yunfei; Hardison, Ross C.; Wang, Yanming; Pugh, B. Franklin

doi:10.1016/j.celrep.2014.06.030

Cited by 65 publications

(80 citation statements)

References 67 publications

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“…(C) xlink-Exo analysis of TFIID binding to wild-type (top panel) and Mu RE/Co (bottom panel) hdm2 DNA. Base pair annotations (Ϯ2 bp) above individual peaks in the line traces (right panel) represent a Ϫ4-bp adjustment to reflect the known inability of exonuclease to cut at locations immediately adjacent to protein/DNA cross-link sites (35). age of TFIID was still bound to the mutant promoters in our single-molecule assays (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…As an alternative approach to studying p53-mediated TFIID/DNA binding, we developed an in vitro formaldehyde-cross-linking/exonuclease mapping assay (xlink-Exo). Our strategy was adapted from a well-established strategy (chromatin immunoprecipitation [ChIP]-exo) to map out protein/DNA contacts of transcription factors in vivo at near-base-pair resolution (35). On the basis of this analysis, TFIID makes extensive contacts with well-characterized core promoter elements (i.e., TATA, InR, MTE, and DPE) on the wild-type hdm2 DNA (Fig.…”

Section: Resultsmentioning

confidence: 99%

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p53 Dynamically Directs TFIID Assembly on Target Gene Promoters

Coleman

Qiao

Singh

et al. 2017

Molecular and Cellular Biology

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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 M ore than 50% of cancer patients harbor p53 mutations, highlighting the essential role of this protein in tumor suppression (1). To properly maintain genomic stability, p53 induces vast gene networks involved in diverse cellular pathways, including the cell cycle arrest, apoptosis, and DNA repair pathways (2). In response to various stress stimuli, p53 acts as a transcriptional activator that specifically binds consensus response elements (REs; two 10-base-pair half-sites [RRRCWWGYYY]) within its target genes to directly stimulate gene expression (2). p53 utilizes its ability to nonspecifically bind and slide along the DNA to expedite the search for target REs (3). Upon recognition of its response genes, p53 facilitates transcription at least in part by targeting the TFIID-mediated transcription machinery to the promoter (4-7). TFIID is composed of TATA-binding protein (TBP) and 14 TBP-associated factors (TAFs). TFIID recognizes and binds multiple core promoter elements (e.g., the TATA box, the initiator, and downstream core promoter elements [DPE]) surrounding the transcription start site (TSS) (8). Once bound, TFIID serves as a central scaffold for six basal factors, including RNA polymerase II, to form a preinitiation complex (PIC) directing transcription initiation. Importantly, without the assistance of activators such as p53, TFIID's core promoter recognition is weak and rate limiting for transcription initiation due to inefficient PIC assembly (9-16). As TFIID is responsible for transcription of at least ϳ90% of proteincoding genes (17), unraveling how p...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

p53 Dynamically Directs TFIID Assembly on Target Gene Promoters

Coleman

Qiao

Singh

et al. 2017

Molecular and Cellular Biology

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“…The EM density representing p53 is highlighted in dark purple, while Pol II is colored gold. Components within this core PIC are color-coded as in He et al (2016) Notably, certain target genes harbor the p53 response elements distal to the core promoter (Chang et al 2014). In these cases, a looping mechanism during transcription activation could be involved.…”

Section: Discussionmentioning

confidence: 99%

“…A recent elegant high-resolution genomewide study on p53's binding to target genes uncovered that Pol II and p53 were in close proximity to its response elements under a variety of stresses (Chang et al 2014). Furthermore, biochemical studies in yeast documented an enrichment of Pol II on target genes in the presence of p53 (Kim et al 2011).…”

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confidence: 99%

Structural visualization of the p53/RNA polymerase II assembly

et al. 2016

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The master tumor suppressor p53 activates transcription in response to various cellular stresses in part by facilitating recruitment of the transcription machinery to DNA. Recent studies have documented a direct yet poorly characterized interaction between p53 and RNA polymerase II (Pol II). Therefore, we dissected the human p53/Pol II interaction via single-particle cryo-electron microscopy, structural docking, and biochemical analyses. This study reveals that p53 binds Pol II via the Rpb1 and Rpb2 subunits, bridging the DNA-binding cleft of Pol II proximal to the upstream DNA entry site. In addition, the key DNA-binding surface of p53, frequently disrupted in various cancers, remains exposed within the assembly. Furthermore, the p53/Pol II cocomplex displays a closed conformation as defined by the position of the Pol II clamp domain. Notably, the interaction of p53 and Pol II leads to increased Pol II elongation activity. These findings indicate that p53 may structurally regulate DNA-binding functions of Pol II via the clamp domain, thereby providing insights into p53-regulated Pol II transcription.

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“…2 The tumor suppressor function of p53 is, however, not entirely attributable to its role in transcription activation, and indeed the majority of p53 binding sites are not associated with a target gene. 4 Both telomeres and p53 play important roles in the maintenance of genome integrity and tumor suppression; however, direct involvement of p53 in telomere function has not been previously described. We recently reported the presence of non-canonical p53 response elements (REs) in the subtelomere region of human and mouse chromosomes.…”

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confidence: 99%