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A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome
Open accessAbstract
The ability to derive a whole-genome map of transcription-factor binding sites (TFBS) is crucial for elucidating gene regulatory networks. Herein, we describe a robust approach that couples chromatin immunoprecipitation (ChIP) with the paired-end ditag (PET) sequencing strategy for unbiased and precise global localization of TFBS. We have applied this strategy to map p53 targets in the human genome. From a saturated sampling of over half a million PET sequences, we characterized 65,572 unique p53 ChIP DNA fragments and established overlapping PET clusters as a readout to define p53 binding loci with remarkable specificity. Based on this information, we refined the consensus p53 binding motif, identified at least 542 binding loci with high confidence, discovered 98 previously unidentified p53 target genes that were implicated in novel aspects of p53 functions, and showed their clinical relevance to p53-dependent tumorigenesis in primary cancer samples.
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“Recent genome-wide analyses have identified from one hundred16 up to thousands17 of potential p53 target genes.”
From Census and evaluation of p53 target genes (2017) · cites this paper as [16]
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Metadata
- Authors
- Wei, C.-L., Wu, Q., Vega, V. B., Chiu, K. P., Ng, P., Zhang, T., Shahab, A., Yong, H. C., Fu, Y., Weng, Z., Liu, J., Zhao, X. D., Chew, J.-L., Lee, Y. L., Kuznetsov, V. A., Sung, W.-K., Miller, L. D., Lim, B., Liu, E. T., Yu, Q., Ng, H.-H., & Ruan, Y.
- Affiliations
- Genome Institute of Singapore (SG)
- Bioinformatics Institute (SG)
- Boston University (US)
- National University of Singapore (SG)
- Harvard University (US)
- Corresponding author
- Ng, Huck-Hui
- Ruan, Yijun
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2006-01
- Volume
- 124
- Issue
- 1
- Pages
- 207-219
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2171407623
- Cited by
- 1,141
- References
- 52
- Citations by year
- 2026: 7 · 2025: 14 · 2024: 11 · 2023: 29 · 2022: 38 · 2021: 30 · 2020: 25 · 2019: 32 · 2018: 38 · 2017: 39 · 2016: 56 · 2015: 43 · 2014: 57 · 2013: 61 · 2012: 66
- FWCI
- 56.35
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 2790 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- National University of Singapore (submittedVersion)
- Funders
- Genome Institute of Singapore
- National Institutes of Health (8r01hg000352-03)
- National Human Genome Research Institute (1R01HG00352-01)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Health Sciences › Medicine › Oncology › Cancer-related Molecular Pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- p53, transcription factor binding sites, ChIP-seq, p53 target genes, gene regulatory networks, cancer, human genome
- MeSH terms
- Binding Sites, Chromosome Mapping, DNA, Humans, Transcription Factors, Tumor Cells, Cultured, Genome, Human, Tumor Suppressor Protein p53, Oligonucleotide Array Sequence Analysis, HCT116 Cells, Chromatin Immunoprecipitation
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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