P53 Pulses Diversify Target Gene Expression Dynamics in an mRNA Half-Life-Dependent Manner and Delineate Co-regulated Target Gene Subnetworks

Joshua R. Porter; Brian E. Fisher; Eric Batchelor

doi:10.1016/j.cels.2016.03.006

P53 Pulses Diversify Target Gene Expression Dynamics in an mRNA Half-Life-Dependent Manner and Delineate Co-regulated Target Gene Subnetworks

Joshua R. Porter, Brian E. Fisher, Eric Batchelor

Research output: Contribution to journal › Article › peer-review

67 Scopus citations

Abstract

The transcription factor p53 responds to DNA double-strand breaks by increasing in concentration in a series of pulses of fixed amplitude, duration, and period. How p53 pulses influence the dynamics of p53 target gene expression is not understood. Here, we show that, in bulk cell populations, patterns of p53 target gene expression cluster into groups with stereotyped temporal behaviors, including pulsing and rising dynamics. These behaviors correlate statistically with the mRNA decay rates of target genes: short mRNA half-lives produce pulses of gene expression. This relationship can be recapitulated by mathematical models of p53-dependent gene expression in single cells and cell populations. Single-cell transcriptional profiling demonstrates that expression of a subset of p53 target genes is coordinated across time within single cells; p53 pulsing attenuates this coordination. These results help delineate how p53 orchestrates the complex DNA damage response and give insight into the function of pulsatile signaling pathways.

Original language	English (US)
Pages (from-to)	272-282
Number of pages	11
Journal	Cell Systems
Volume	2
Issue number	4
DOIs	https://doi.org/10.1016/j.cels.2016.03.006
State	Published - Apr 27 2016
Externally published	Yes

Bibliographical note

Funding Information:
This research was supported by the Intramural Research Program of the NIH, National Cancer Institute, CCR.

Funding Information:
We thank W. Telford and V. Kapoor in the Center for Cancer Research (CCR) ETIB Flow Cytometry Core for aid in single-cell sorting as well as M. Raffeld and the CCR Molecular Diagnostics Unit and J. Zhu and the National Heart, Lung, and Blood Institute DNA Sequencing and Genomics Core for help with single cell transcriptional profiling. We also thank D. Levens, the Levens lab, A. Moody, A. Sun, T. Przytycka, C. Parent, J. Oberholtzer, A. Loewer, L. Goentoro, J. Hansen, J. Stommel, and J. Luo for helpful discussions. This research was supported by the Intramural Research Program of the NIH, National Cancer Institute, CCR.

Publisher Copyright:
© 2016 Elsevier Inc.

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10.1016/j.cels.2016.03.006

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abstract = "The transcription factor p53 responds to DNA double-strand breaks by increasing in concentration in a series of pulses of fixed amplitude, duration, and period. How p53 pulses influence the dynamics of p53 target gene expression is not understood. Here, we show that, in bulk cell populations, patterns of p53 target gene expression cluster into groups with stereotyped temporal behaviors, including pulsing and rising dynamics. These behaviors correlate statistically with the mRNA decay rates of target genes: short mRNA half-lives produce pulses of gene expression. This relationship can be recapitulated by mathematical models of p53-dependent gene expression in single cells and cell populations. Single-cell transcriptional profiling demonstrates that expression of a subset of p53 target genes is coordinated across time within single cells; p53 pulsing attenuates this coordination. These results help delineate how p53 orchestrates the complex DNA damage response and give insight into the function of pulsatile signaling pathways.",

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P53 Pulses Diversify Target Gene Expression Dynamics in an mRNA Half-Life-Dependent Manner and Delineate Co-regulated Target Gene Subnetworks

Abstract

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