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Sustained oscillations of NF-kappaB produce distinct genome scanning and gene expression profiles.

Sung MH, Salvatore L, De Lorenzi R, Indrawan A, Pasparakis M, Hager GL, Bianchi ME, Agresti A - PLoS ONE (2009)

Bottom Line: Mathematical modeling suggests that NF-kappaB oscillations are selected over other non-oscillatory dynamics by fine-tuning the relative strengths of feedback loops like IkappaBalpha.Perturbation of long-term NF-kappaB oscillations interfered with its short-term interaction with chromatin and balanced transcriptional output, as predicted by the mathematical model.We propose that negative feedback loops do not simply terminate signaling, but rather promote oscillations of NF-kappaB in the nucleus, and these oscillations are functionally advantageous.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America. sungm@mail.nih.gov

ABSTRACT
NF-kappaB is a prototypic stress-responsive transcription factor that acts within a complex regulatory network. The signaling dynamics of endogenous NF-kappaB in single cells remain poorly understood. To examine real time dynamics in living cells, we monitored NF-kappaB activities at multiple timescales using GFP-p65 knock-in mouse embryonic fibroblasts. Oscillations in NF-kappaB were sustained in most cells, with several cycles of transient nuclear translocation after TNF-alpha stimulation. Mathematical modeling suggests that NF-kappaB oscillations are selected over other non-oscillatory dynamics by fine-tuning the relative strengths of feedback loops like IkappaBalpha. The ability of NF-kappaB to scan and interact with the genome in vivo remained remarkably constant from early to late cycles, as observed by fluorescence recovery after photobleaching (FRAP). Perturbation of long-term NF-kappaB oscillations interfered with its short-term interaction with chromatin and balanced transcriptional output, as predicted by the mathematical model. We propose that negative feedback loops do not simply terminate signaling, but rather promote oscillations of NF-kappaB in the nucleus, and these oscillations are functionally advantageous.

Show MeSH
Fine-tuning transcriptional output by NF-κB oscillations.(A) When there are little or no NF-κB oscillations, immediately accessible target genes are continuously induced. Gene-specific mechanisms attenuate the transcription of these genes over time, while a different group of genes become responsive. In this model, overall gene expression kinetics does not critically depend on NF-κB dynamics. (B) Sustained NF-κB oscillations allow only pulses of expression for the immediate early genes, as the transcription factor interacts transiently with the chromatin at discrete times. In later signaling cycles, NF-κB returns with characteristic genome-scanning competency and acts on late-accessible genes, without having accumulated early transcripts at a high level. Therefore, NF-κB oscillations, which are strongly coupled with upstream signaling kinetics, ensure balanced gene expression programs.
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pone-0007163-g007: Fine-tuning transcriptional output by NF-κB oscillations.(A) When there are little or no NF-κB oscillations, immediately accessible target genes are continuously induced. Gene-specific mechanisms attenuate the transcription of these genes over time, while a different group of genes become responsive. In this model, overall gene expression kinetics does not critically depend on NF-κB dynamics. (B) Sustained NF-κB oscillations allow only pulses of expression for the immediate early genes, as the transcription factor interacts transiently with the chromatin at discrete times. In later signaling cycles, NF-κB returns with characteristic genome-scanning competency and acts on late-accessible genes, without having accumulated early transcripts at a high level. Therefore, NF-κB oscillations, which are strongly coupled with upstream signaling kinetics, ensure balanced gene expression programs.

Mentions: Consistent with this hypothesis, p65 mobility by FRAP, reflecting its chromatin residence time, is maintained through the recurrent NF-κB cycles, and is sensitive to perturbations of the natural oscillations. Moreover, such perturbations also alter the transcription of targets, from early to late genes. The late cycles, absent in LMB co-treatment, contribute significantly to late gene expression, while continuous presence of active NF-κB in the nucleus in CHX co-treatment produces exaggerated transcriptional responses. These results suggest that the oscillatory mode of NF-κB action may be a cellular trade-off between efficient pulse expression of immediate early genes and the need for NF-κB to monitor the signaling status for several hours before acting on the modified chromatin landscape [29], [30] (Fig. 7). Limiting the transcription of the immediate genes by periodic inactivity is important in various signaling contexts, especially because many of these encode secreted cytokines and chemokines. Their overproduction would be dangerous in vivo with far-reaching consequences. In summary, fast transient interaction with the chromatin, continuous nucleocytoplasmic shuttling, and long-term oscillations are distinct but inter-dependent mechanisms in functional signaling by NF-κB (compare models in Fig. 7).


Sustained oscillations of NF-kappaB produce distinct genome scanning and gene expression profiles.

Sung MH, Salvatore L, De Lorenzi R, Indrawan A, Pasparakis M, Hager GL, Bianchi ME, Agresti A - PLoS ONE (2009)

Fine-tuning transcriptional output by NF-κB oscillations.(A) When there are little or no NF-κB oscillations, immediately accessible target genes are continuously induced. Gene-specific mechanisms attenuate the transcription of these genes over time, while a different group of genes become responsive. In this model, overall gene expression kinetics does not critically depend on NF-κB dynamics. (B) Sustained NF-κB oscillations allow only pulses of expression for the immediate early genes, as the transcription factor interacts transiently with the chromatin at discrete times. In later signaling cycles, NF-κB returns with characteristic genome-scanning competency and acts on late-accessible genes, without having accumulated early transcripts at a high level. Therefore, NF-κB oscillations, which are strongly coupled with upstream signaling kinetics, ensure balanced gene expression programs.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2747007&req=5

pone-0007163-g007: Fine-tuning transcriptional output by NF-κB oscillations.(A) When there are little or no NF-κB oscillations, immediately accessible target genes are continuously induced. Gene-specific mechanisms attenuate the transcription of these genes over time, while a different group of genes become responsive. In this model, overall gene expression kinetics does not critically depend on NF-κB dynamics. (B) Sustained NF-κB oscillations allow only pulses of expression for the immediate early genes, as the transcription factor interacts transiently with the chromatin at discrete times. In later signaling cycles, NF-κB returns with characteristic genome-scanning competency and acts on late-accessible genes, without having accumulated early transcripts at a high level. Therefore, NF-κB oscillations, which are strongly coupled with upstream signaling kinetics, ensure balanced gene expression programs.
Mentions: Consistent with this hypothesis, p65 mobility by FRAP, reflecting its chromatin residence time, is maintained through the recurrent NF-κB cycles, and is sensitive to perturbations of the natural oscillations. Moreover, such perturbations also alter the transcription of targets, from early to late genes. The late cycles, absent in LMB co-treatment, contribute significantly to late gene expression, while continuous presence of active NF-κB in the nucleus in CHX co-treatment produces exaggerated transcriptional responses. These results suggest that the oscillatory mode of NF-κB action may be a cellular trade-off between efficient pulse expression of immediate early genes and the need for NF-κB to monitor the signaling status for several hours before acting on the modified chromatin landscape [29], [30] (Fig. 7). Limiting the transcription of the immediate genes by periodic inactivity is important in various signaling contexts, especially because many of these encode secreted cytokines and chemokines. Their overproduction would be dangerous in vivo with far-reaching consequences. In summary, fast transient interaction with the chromatin, continuous nucleocytoplasmic shuttling, and long-term oscillations are distinct but inter-dependent mechanisms in functional signaling by NF-κB (compare models in Fig. 7).

Bottom Line: Mathematical modeling suggests that NF-kappaB oscillations are selected over other non-oscillatory dynamics by fine-tuning the relative strengths of feedback loops like IkappaBalpha.Perturbation of long-term NF-kappaB oscillations interfered with its short-term interaction with chromatin and balanced transcriptional output, as predicted by the mathematical model.We propose that negative feedback loops do not simply terminate signaling, but rather promote oscillations of NF-kappaB in the nucleus, and these oscillations are functionally advantageous.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America. sungm@mail.nih.gov

ABSTRACT
NF-kappaB is a prototypic stress-responsive transcription factor that acts within a complex regulatory network. The signaling dynamics of endogenous NF-kappaB in single cells remain poorly understood. To examine real time dynamics in living cells, we monitored NF-kappaB activities at multiple timescales using GFP-p65 knock-in mouse embryonic fibroblasts. Oscillations in NF-kappaB were sustained in most cells, with several cycles of transient nuclear translocation after TNF-alpha stimulation. Mathematical modeling suggests that NF-kappaB oscillations are selected over other non-oscillatory dynamics by fine-tuning the relative strengths of feedback loops like IkappaBalpha. The ability of NF-kappaB to scan and interact with the genome in vivo remained remarkably constant from early to late cycles, as observed by fluorescence recovery after photobleaching (FRAP). Perturbation of long-term NF-kappaB oscillations interfered with its short-term interaction with chromatin and balanced transcriptional output, as predicted by the mathematical model. We propose that negative feedback loops do not simply terminate signaling, but rather promote oscillations of NF-kappaB in the nucleus, and these oscillations are functionally advantageous.

Show MeSH