Cited by 1,141Genomics and Chromatin DynamicsCancer-related Molecular PathwaysChromatin Remodeling and Cancer

A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome

Open access
Wei, Chia-Lin, Wu, Qiang, Vega, Vinsensius B., Chiu, Kuo Ping, Ng, Patrick, Zhang, Tao, Shahab, Atif, Yong, How Choong +14 more·2006·Cell

Abstract

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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Crossref · 10.1016/j.cell.2005.10.043

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  • Recent genome-wide analyses have identified from one hundred up to thousands of potential p53 target genes.

    “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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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
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
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

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