The DOI matches its Crossref record; 51 of the 52 references it cites were found in a registry or an index.
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]
Citations
Cites
WAF1, a potential mediator of p53 tumor suppression
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Genome sequencing in microfabricated high-density picolitre reactors
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“, 2004) or are well-known p53 targets (Polyak et al., 1997; Vogelstein et al., 2000).”
BackgroundInfluentialFinishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03001 · Cited by 4,971
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Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
A model for p53-induced apoptosis
Polyak, K., Xia, Y., Zweier, J. L., Kinzler, K. W., & Vogelstein, B. (1997) · Nature · doi:10.1038/38525 · Cited by 2,500
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Research works printed but not linked: 1
- Kuznetsov, 2005, Mathematical Analysis and Modeling of SAGE Transcriptome, 139
Cited by
Sorted by citations
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
Self-citationBlinded by the Light: The Growing Complexity of p53
Vousden, K. H., & Prives, C. (2009) · Cell · doi:10.1016/j.cell.2009.04.037 · Cited by 3,163
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927
Mapping and analysis of chromatin state dynamics in nine human cell types
Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898
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
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