Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells
Open accessAbstract
The effects of diverse stresses on promoter selectivity and transcription regulation by the tumor suppressor p53 are poorly understood. We have taken a comprehensive approach to characterizing the human p53 network that includes p53 levels, binding, expression and chromatin changes under diverse stresses. Human osteosarcoma U2OS cells treated with anti-cancer drugs Doxorubicin (DXR) or Nutlin-3 (Nutlin) led to strikingly different p53 gene binding patterns based on chromatin immunoprecipitation with high-throughput sequencing experiments. Although two contiguous RRRCWWGYYY decamers is the consensus binding motif, p53 can bind a single decamer and function in vivo. Although the number of sites bound by p53 was six times greater for Nutlin than DXR, expression changes induced by Nutlin were much less dramatic compared with DXR. Unexpectedly, the solvent dimethylsulphoxide (DMSO) alone induced p53 binding to many sites common to DXR; however, this binding had no effect on target gene expression. Together, these data imply a two-stage mechanism for p53 transactivation where p53 binding only constitutes the first stage. Furthermore, both p53 binding and transactivation were associated with increased active histone modification histone H3 lysine 4 trimethylation. We discovered 149 putative new p53 target genes including several that are relevant to tumor suppression, revealing potential new targets for cancer therapy and expanding our understanding of the p53 regulatory network.
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p53 directly induces numerous genes involved in triggering the recruitment of immune cells and immune surveillance in human cells, which can involve the TLR gene family.
“gene expression analyses has shown that p53 directly induces numerous genes involved in triggering the recruitment of immune cells and immune surveillance in human cells [11], which can involve the TLR gene family.”
From Ligand dependent restoration of human TLR3 signaling and death in p53 mutant cells (2016) · cites this paper as [11]
The Introduction says p53 can transactivate genes involved in innate immune responses, and the Results (Novel p53 target genes; page unavailable) identify many putative direct p53 targets in human cancer cells. Our copy does not establish that numerous targets trigger immune-cell recruitment or immune surveillance, or identify the TLR gene family as part of that finding. (LLM, conf=0.83)
Experimental — accuracy not yet measuredResults from multiple studies suggest that p53 can bind and transactivate target genes through noncanonical binding sites, particularly through half-sites.
“In addition, results from multiple studies suggest that p53 can bind and transactivate target genes through noncanonical binding sites, particularly through half-sites.22, 54, 55, 56”
From Census and evaluation of p53 target genes (2017) · cites this paper as [22]
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Self-citation
- Authors
- Menendez, D., Nguyen, T.-A., Freudenberg, J. M., Mathew, V. J., Anderson, C. W., Jothi, R., & Resnick, M. A.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Jothi, Raja
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-06-17
- Volume
- 41
- Issue
- 15
- Pages
- 7286-7301
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3753631
- OpenAlex
- W2118254139
- Cited by
- 154
- References
- 71
- Citations by year
- 2026: 5 · 2025: 7 · 2024: 11 · 2023: 16 · 2022: 8 · 2021: 7 · 2020: 9 · 2019: 6 · 2018: 4 · 2017: 26 · 2016: 14 · 2015: 17 · 2014: 24
- FWCI
- 9.82
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- Funders
- Johns Hopkins University
- National Institutes of Health
- U.S. Public Health Service (1ZIAES102625-04)
- National Institute of Environmental Health Sciences (Z01ES065079, ZIAES102625)
- Topics
- Health Sciences › Medicine › Oncology › Cancer-related Molecular Pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- p53, p53 binding sites, p53 transactivation, transcriptional regulation, stress response, doxorubicin, nutlin, dimethyl sulfoxide, p53 target genes, histone H3 lysine 4 trimethylation, chromatin, osteosarcoma, tumor suppression
- MeSH terms
- Antineoplastic Agents, Binding Sites, Dimethyl Sulfoxide, DNA, Neoplasm, Doxorubicin, Histones, Humans, Imidazoles, Methylation, Piperazines, Promoter Regions, Genetic, Protein Binding, Osteosarcoma, Transcriptional Activation, Gene Expression Regulation, Neoplastic, Genes, p53, Tumor Suppressor Protein p53, Consensus Sequence, HCT116 Cells, Gene Regulatory Networks, Nucleotide Motifs
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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