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

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

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Wei, Chia-Lin, Wu, Qiang, Vega, Vinsensius B., Chiu, Kuo Ping, Ng, Patrick, Zhang, Tao, Shahab, Atif, Yong, How Choong, Fu, YuTao, Weng, Zhiping, Liu, JianJun, Zhao, Xiao Dong, Chew, Joon-Lin, Lee, Yen Ling, Kuznetsov, Vladimir A., Sung, Wing-Kin, Miller, Lance D., Lim, Bing, Liu, Edison T., Yu, Qiang, Ng, Huck-Hui, Ruan, Yijun·2006·Cell

DOI 10.1016/j.cell.2005.10.043

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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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Self-citation

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: Wei, Chia-Lin
Wu, Qiang
Zhang, Tao
Shahab, Atif
Weng, Zhiping
Liu, JianJun
Zhao, Xiao Dong
Kuznetsov, Vladimir A.
Sung, Wing-Kin
Miller, Lance D.
Lim, Bing
Liu, Edison T.
Yu, Qiang
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)
DOI: 10.1016/j.cell.2005.10.043
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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A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome

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