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A functional map of NFkappaB signaling identifies novel modulators and multiple system controls.

Halsey TA, Yang L, Walker JR, Hogenesch JB, Thomas RS - Genome Biol. (2007)

Bottom Line: The expression of the modulators at the RNA level was distributed disproportionately across tissues, providing flexibility in network structure, and the number of positive and negative modulators present in a given tissue was highly correlated, suggesting that positive and negative regulation is balanced at the tissue level.The relative locations of the modulators are consistent with an hourglass structure for the NFkappaB network that is characteristic of robust systems.The tissue distribution of the modulators and downstream location of the negative modulators serve as layers of control within the system that allow differential responses to different stimuli.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Hamner Institutes for Health Sciences, 6 Davis Drive, PO Box 12137, Research Triangle Park, NC 27709-2137, USA.

ABSTRACT

Background: The network of signaling pathways that leads to activation of the NFkappaB transcription factors is a branched structure with different inputs and cross-coupling with other signaling pathways. How these signals are integrated to produce specific, yet diverse responses is not clearly understood. To identify the components and structural features of the NFkappaB network, a series of cell-based, genomic screens was performed using a library of approximately 14,500 full-length genes.

Results: A total of 154 positive and 88 negative modulators of NFkappaB signaling were identified. Using a series of dominant-negative constructs and functional assays, these modulators were mapped to the known NFkappaB signaling cascade. Most of the positive modulators acted upstream of the IkappaB kinase complex, supporting previous observations that the IkappaB kinases represent the primary point of convergence in the network. A number of negative modulators were localized downstream of the IkappaB kinase beta (IKBKB) subunit, suggesting that they form an additional layer of negative control within the system. The expression of the modulators at the RNA level was distributed disproportionately across tissues, providing flexibility in network structure, and the number of positive and negative modulators present in a given tissue was highly correlated, suggesting that positive and negative regulation is balanced at the tissue level.

Conclusion: The relative locations of the modulators are consistent with an hourglass structure for the NFkappaB network that is characteristic of robust systems. The tissue distribution of the modulators and downstream location of the negative modulators serve as layers of control within the system that allow differential responses to different stimuli.

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Contextual organization of the NFκB negative modulators. Organization was determined on the basis of follow-up screens with an IKBKB constitutively-active mutant. If activation of the NFκB reporter was blocked by the negative modulator (≥ 70% average reduction), the negative modulator was considered downstream of the constitutively active mutant. If activation of the NFκB reporter was not blocked, the negative modulator was considered unclassified as to its inhibitor influence.
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Figure 5: Contextual organization of the NFκB negative modulators. Organization was determined on the basis of follow-up screens with an IKBKB constitutively-active mutant. If activation of the NFκB reporter was blocked by the negative modulator (≥ 70% average reduction), the negative modulator was considered downstream of the constitutively active mutant. If activation of the NFκB reporter was not blocked, the negative modulator was considered unclassified as to its inhibitor influence.

Mentions: To assess the relative location of the negative modulators, each modulator was screened together with a constitutively active IKBKB mutant (Additional data file 4). If activation of the NFκB reporter was blocked by the negative modulator (≥ 70% reduction), the negative modulator was considered downstream of the constitutively active mutant. If activation of the NFκB reporter was not blocked, the negative modulator was considered unclassified as to its inhibitor influence. For the group of negative modulators downstream of IKBKB, several genes were identified that were previously demonstrated to inhibit NFκB signaling (Figure 5). These genes include NFKBIB, NFKBIE, PIAS3, PRKACG, PTGER2, and PTGER4. The downstream effects of the two IκB genes (NFKBIB, NFKBIE) have been well established [2], whereas PIAS3 functions downstream by binding to RELA and suppressing NFκB-dependent transcription [44]. The gamma catalytic subunit of protein kinase A (PRKACG) has been shown to repress NFκB signaling by phosphorylating the p50 homodimer, which acts a transcriptional repressor by maintaining DNA binding in unstimulated cells [45]. Finally, for the PTGER2 and PTGER4 genes, a clear mechanism has not been elucidated, but a recent report by Akaogi and colleagues [46] showed that the NFκB-dependent transcription of TNF was inhibited by 70% in response to activation of prostaglandin E2 and E4 receptors.


A functional map of NFkappaB signaling identifies novel modulators and multiple system controls.

Halsey TA, Yang L, Walker JR, Hogenesch JB, Thomas RS - Genome Biol. (2007)

Contextual organization of the NFκB negative modulators. Organization was determined on the basis of follow-up screens with an IKBKB constitutively-active mutant. If activation of the NFκB reporter was blocked by the negative modulator (≥ 70% average reduction), the negative modulator was considered downstream of the constitutively active mutant. If activation of the NFκB reporter was not blocked, the negative modulator was considered unclassified as to its inhibitor influence.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2394752&req=5

Figure 5: Contextual organization of the NFκB negative modulators. Organization was determined on the basis of follow-up screens with an IKBKB constitutively-active mutant. If activation of the NFκB reporter was blocked by the negative modulator (≥ 70% average reduction), the negative modulator was considered downstream of the constitutively active mutant. If activation of the NFκB reporter was not blocked, the negative modulator was considered unclassified as to its inhibitor influence.
Mentions: To assess the relative location of the negative modulators, each modulator was screened together with a constitutively active IKBKB mutant (Additional data file 4). If activation of the NFκB reporter was blocked by the negative modulator (≥ 70% reduction), the negative modulator was considered downstream of the constitutively active mutant. If activation of the NFκB reporter was not blocked, the negative modulator was considered unclassified as to its inhibitor influence. For the group of negative modulators downstream of IKBKB, several genes were identified that were previously demonstrated to inhibit NFκB signaling (Figure 5). These genes include NFKBIB, NFKBIE, PIAS3, PRKACG, PTGER2, and PTGER4. The downstream effects of the two IκB genes (NFKBIB, NFKBIE) have been well established [2], whereas PIAS3 functions downstream by binding to RELA and suppressing NFκB-dependent transcription [44]. The gamma catalytic subunit of protein kinase A (PRKACG) has been shown to repress NFκB signaling by phosphorylating the p50 homodimer, which acts a transcriptional repressor by maintaining DNA binding in unstimulated cells [45]. Finally, for the PTGER2 and PTGER4 genes, a clear mechanism has not been elucidated, but a recent report by Akaogi and colleagues [46] showed that the NFκB-dependent transcription of TNF was inhibited by 70% in response to activation of prostaglandin E2 and E4 receptors.

Bottom Line: The expression of the modulators at the RNA level was distributed disproportionately across tissues, providing flexibility in network structure, and the number of positive and negative modulators present in a given tissue was highly correlated, suggesting that positive and negative regulation is balanced at the tissue level.The relative locations of the modulators are consistent with an hourglass structure for the NFkappaB network that is characteristic of robust systems.The tissue distribution of the modulators and downstream location of the negative modulators serve as layers of control within the system that allow differential responses to different stimuli.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Hamner Institutes for Health Sciences, 6 Davis Drive, PO Box 12137, Research Triangle Park, NC 27709-2137, USA.

ABSTRACT

Background: The network of signaling pathways that leads to activation of the NFkappaB transcription factors is a branched structure with different inputs and cross-coupling with other signaling pathways. How these signals are integrated to produce specific, yet diverse responses is not clearly understood. To identify the components and structural features of the NFkappaB network, a series of cell-based, genomic screens was performed using a library of approximately 14,500 full-length genes.

Results: A total of 154 positive and 88 negative modulators of NFkappaB signaling were identified. Using a series of dominant-negative constructs and functional assays, these modulators were mapped to the known NFkappaB signaling cascade. Most of the positive modulators acted upstream of the IkappaB kinase complex, supporting previous observations that the IkappaB kinases represent the primary point of convergence in the network. A number of negative modulators were localized downstream of the IkappaB kinase beta (IKBKB) subunit, suggesting that they form an additional layer of negative control within the system. The expression of the modulators at the RNA level was distributed disproportionately across tissues, providing flexibility in network structure, and the number of positive and negative modulators present in a given tissue was highly correlated, suggesting that positive and negative regulation is balanced at the tissue level.

Conclusion: The relative locations of the modulators are consistent with an hourglass structure for the NFkappaB network that is characteristic of robust systems. The tissue distribution of the modulators and downstream location of the negative modulators serve as layers of control within the system that allow differential responses to different stimuli.

Show MeSH