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Nucleic Acids Res. 2018 Sep 19;46(16):8153-8167. doi: 10.1093/nar/gky720.

Revealing a human p53 universe.

Author information

1
Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences/National Institutes of Health, Research Triangle Park, NC 27709, USA.
2
Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences/National Institutes of Health, Research Triangle Park, NC 27709, USA.
3
Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences/National Institutes of Health, Research Triangle Park, NC 27709, USA.
4
Office of Scientific Computing, National Institute of Environmental Health Sciences/National Institutes of Health, Research Triangle Park, NC 27709, USA.

Abstract

p53 transcriptional networks are well-characterized in many organisms. However, a global understanding of requirements for in vivo p53 interactions with DNA and relationships with transcription across human biological systems in response to various p53 activating situations remains limited. Using a common analysis pipeline, we analyzed 41 data sets from genome-wide ChIP-seq studies of which 16 have associated gene expression data, including our recent primary data with normal human lymphocytes. The resulting extensive analysis, accessible at p53 BAER hub via the UCSC browser, provides a robust platform to characterize p53 binding throughout the human genome including direct influence on gene expression and underlying mechanisms. We establish the impact of spacers and mismatches from consensus on p53 binding in vivo and propose that once bound, neither significantly influences the likelihood of expression. Our rigorous approach revealed a large p53 genome-wide cistrome composed of >900 genes directly targeted by p53. Importantly, we identify a core cistrome signature composed of genes appearing in over half the data sets, and we identify signatures that are treatment- or cell-specific, demonstrating new functions for p53 in cell biology. Our analysis reveals a broad homeostatic role for human p53 that is relevant to both basic and translational studies.

PMID:
30107566
PMCID:
PMC6144829
DOI:
10.1093/nar/gky720
[Indexed for MEDLINE]
Free PMC Article

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