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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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Cites
WAF1, a potential mediator of p53 tumor suppression
El-Deiry, W. S., Tokino, T., Velculescu, V. E., Levy, D. B., Parsons, R., Trent, J. M., Lin, D., Mercer, W. E., Kinzler, K. W., & Vogelstein, B. (1993) · Cell · doi:10.1016/0092-8674(93)90500-p · Cited by 8,321
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693
Vogelstein, B., Lane, D., & Levine, A. J. (2000) · Nature · doi:10.1038/35042675 · Cited by 6,607 · cited 3×
“, 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
Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells
Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., Guenther, M. G., Kumar, R. M., Murray, H. L., Jenner, R. G., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.020 · Cited by 4,505
Capturing Chromosome Conformation
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
The ENCODE (ENCyclopedia Of DNA Elements) Project
(2004) · Science · doi:10.1126/science.1105136 · Cited by 2,390
Definition of a consensus binding site for p53
El-Deiry, W. S., Kern, S. E., Pietenpol, J. A., Kinzler, K. W., & Vogelstein, B. (1992) · Nature Genetics · doi:10.1038/ng0492-45 · Cited by 1,985
Genome-Wide Location and Function of DNA Binding Proteins
Ren, B., Robert, F., Wyrick, J. J., Aparicio, O. M., Jennings, E. G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N. M., Kanin, E. I., et al. (2000) · Science · doi:10.1126/science.290.5500.2306 · Cited by 1,768
Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome
Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X., McCutcheon, J. P., Rosenbaum, A. M., Wang, M. D., Zhang, K., Mitra, R. D., & Church, G. M. (2005) · Science · doi:10.1126/science.1117389 · Cited by 1,402
Carroll, J. S., Liu, X. S., Brodsky, A. S., Li, W., Meyer, C. A., Szary, A. J., Eeckhoute, J., Shao, W., Hestermann, E. V., Geistlinger, T. R., et al. (2005) · Cell · doi:10.1016/j.cell.2005.05.008 · Cited by 1,384
Miller, L. D., Smeds, J., George, J., Vega, V. B., Vergara, L. A., Ploner, A., Yudi Pawitan, Y., Hall, P. N., Klaar, S., Liu, E. T., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506230102 · Cited by 1,256
Self-citationTRANSFAC: an integrated system for gene expression regulation
Wingender, E. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.316 · Cited by 1,249
Ng, H., Robert, F., Young, R. A., & Struhl, K. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00092-3 · Cited by 1,131
Self-citationCawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. (2004) · Cell · doi:10.1016/s0092-8674(04)00127-8 · Cited by 1,095
Self-citationA high-resolution map of active promoters in the human genome
Kim, T. H., Barrera, L. O., Zheng, M., Qu, C., Singer, M. A., Richmond, T., Wu, Y., Green, R. D., & Ren, B. (2005) · Nature · doi:10.1038/nature03877 · Cited by 954
Impey, S., McCorkle, S., Cha‐Molstad, H., Dwyer, J. M., Yochum, G. S., Boss, J. M., McWeeney, S. K., Dunn, J. J., Mandel, G., & Goodman, R. H. (2004) · Cell · doi:10.1016/j.cell.2004.10.032 · Cited by 708
Analysis of p53-regulated gene expression patterns using oligonucleotide arraysPreprint
Zhao, R., Gish, K., Murphy, M. E., Yin, Y., Notterman, D. A., Hoffman, W. H., Tom, E., Mack, D. H., & Levine, A. J. (2000) · Genes & Development · doi:10.1101/gad.14.8.981 · Cited by 632
Thompson, E. W., Paik, S., Brünner, N., Sommers, C. L., Zugmaier, G., Clarke, R. C., Shima, T. B., Torri, J. A., Donahue, S., Lippman, M. E., et al. (1992) · Journal of Cellular Physiology · doi:10.1002/jcp.1041500314 · Cited by 522
Active chromatin domains are defined by acetylation islands revealed by genome-wide mappingPreprint
Roh, T., Cuddapah, S., & Zhao, K. (2005) · Genes & Development · doi:10.1101/gad.1272505 · Cited by 469
Bergh, J. C. S., Norberg, T., Sjögren, S., Lindgren, A., & Holmberg, L. (1995) · Nature Medicine · doi:10.1038/nm1095-1029 · Cited by 456
Identification and classification of p53-regulated genes
Yu, J., Zhang, L., Hwang, P. M., Rago, C., Kinzler, K. W., & Vogelstein, B. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.25.14517 · Cited by 451
Weinmann, A. S., Yan, P. S., Oberley, M. J., Huang, T. H. ‐., & Farnham, P. (2002) · Genes & Development · doi:10.1101/gad.943102 · Cited by 443
Use of Chromatin Immunoprecipitation To Clone Novel E2F Target Promoters
Weinmann, A. S., Bartley, S. M., Zhang, T., Zhang, M. Q., & Farnham, P. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.20.6820-6832.2001 · Cited by 383
Self-citationWeinmann, A. S., & Farnham, P. (2002) · Methods · doi:10.1016/s1046-2023(02)00006-3 · Cited by 343
DNA microarrays identification of primary and secondary target genes regulated by p53
Kannan, K., Amariglio, N., Rechavi, G., Jacob‐Hirsch, J., Kela, I., Kaminski, N., Getz, G. A., Domany, E., & Givol, D. (2001) · Oncogene · doi:10.1038/sj.onc.1204319 · Cited by 330
Kaeser, M. D., & Iggo, R. D. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.012283399 · Cited by 302
Remote control of gene transcription
West, A. G., & Fraser, P. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi104 · Cited by 302
The p53MH algorithm and its application in detecting p53-responsive genes
Hoh, J., Jin, S. V., Parrado, T., Edington, J., Levine, A. J., & Ott, J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.132268899 · Cited by 295
Ng, P., Wei, C., Sung, W.-K. K., Chiu, K. P., Lipovich, L., Ang, C. C., Gupta, S. M., Shahab, A., Ridwan, A. B. M., Wong, C., et al. (2005) · Nature Methods · doi:10.1038/nmeth733 · Cited by 250
Self-citationWells, J. M., & Farnham, P. (2002) · Methods · doi:10.1016/s1046-2023(02)00007-5 · Cited by 240
Bnip3L is induced by p53 under hypoxia, and its knockdown promotes tumor growth
Fei, P., Wang, W., Kim, S.-H., Wang, S., Burns, T. F., Sax, J. K., Buzzai, M., Dicker, D. T., McKenna, W. G., Bernhard, E. J., et al. (2004) · Cancer Cell · doi:10.1016/j.ccr.2004.10.012 · Cited by 236
p53 regulates cell survival by inhibiting PIK3CA in squamous cell carcinomasPreprint
Singh, B., Reddy, P. G., Goberdhan, A., Walsh, C., Dao, S., Ngai, I. M., Chou, T., O‐charoenrat, P., Levine, A. J., Rao, P. H., et al. (2002) · Genes & Development · doi:10.1101/gad.973602 · Cited by 219
Finding functional sequence elements by multiple local alignment
Frith, M. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh169 · Cited by 198
Mirza, A., Wu, Q. J., Wang, L., McClanahan, T., Bishop, W. R., Gheyas, F., Ding, W., Hutchins, B., Hockenberry, T., Kirschmeier, P. T., et al. (2003) · Oncogene · doi:10.1038/sj.onc.1206477 · Cited by 183
Self-citationGATA-1 binding sites mapped in the β-globin locus by using mammalian chIp-chip analysis
Horak, C. E., Mahajan, M. C., Luscombe, N. M., Gerstein, M., Weissman, S. M., & Snyder, M. P. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052706999 · Cited by 153
PAC1 phosphatase is a transcription target of p53 in signalling apoptosis and growth suppression
Yin, Y., Liu, Y., Jin, Y. J., Hall, E. J., & Barrett, J. C. (2003) · Nature · doi:10.1038/nature01519 · Cited by 145
Regulation of cell migration and survival by focal adhesion targeting of Lasp-1
Lin, Y. H., Park, Z., Lin, D., Brahmbhatt, A. A., Rio, M., Yates, J. R., & Klemke, R. L. (2004) · The Journal of Cell Biology · doi:10.1083/jcb.200311045 · Cited by 142
p53-regulated Transcriptional Program Associated with Genotoxic Stress-induced Apoptosis
Kho, P. S., Wang, Z., Zhuang, L., Li, Y., Chew, J.-L., Ng, H., Liu, E. T., & Yu, Q. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m311912200 · Cited by 142
Self-citationHaverty, P. M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh183 · Cited by 112
Chen, J., & Sadowski, I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407069102 · Cited by 111
Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment
Kim, J., Bhinge, A., Morgan, X. C., & Iyer, V. R. (2004) · Nature Methods · doi:10.1038/nmeth726 · Cited by 106
Cell-adhesion-dependent influences on genomic instability and carcinogenesis
Tlsty, T. D. (1998) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(98)80041-0 · Cited by 101
Yoon, H., Liyanarachchi, S., Wright, F. A., Davuluri, R. V., Lockman, J. C., de la Chapelle, A., & Pellegata, N. S. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.242597299 · Cited by 95
Coates, P. J., Lorimore, S. A., Lindsay, K. J., & Wright, E. G. (2003) · The Journal of Pathology · doi:10.1002/path.1456 · Cited by 65
Peroxisomes: Another Branch of the Secretory Pathway?
Schekman, R. W. (2005) · Cell · doi:10.1016/j.cell.2005.06.033 · Cited by 60
A Chromatin Immunoprecipitation Screen Reveals Protein Kinase Cβ as a Direct RUNX1 Target Gene
Hug, B. A., Ahmed, N., Robbins, J. A., & Lazar, M. A. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m309524200 · Cited by 45
Sage: Current Technologies and Applications
Wang, S. M. (2005) · Cited by 16
Crosby, M. E., Oancea, M., & Almasan, A. (2004) · Journal of Environmental Pathology Toxicology and Oncology · doi:10.1615/jenvpathtoxoncol.v23.i1.70 · Cited by 12
SAGE: Current Technologies and Applications
Kang, J., & Hwang, P. M. (2006) · Expert Review of Molecular Diagnostics · doi:10.1586/14737159.6.2.137 · Cited by 10
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1 of the 52 references couldn’t be matched to a known paper.
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- Kuznetsov, 2005, Mathematical Analysis and Modeling of SAGE Transcriptome, 139
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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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