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Review article

In vivo binding of NF-κB to the IκBβ promoter is insufficient for transcriptional activation

Bryan D. Griffin, Paul N. Moynagh
Biochemical Journal Nov 15, 2006, 400 (1) 115-125; DOI: 10.1042/BJ20060786
Bryan D. Griffin
UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Paul N. Moynagh
UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Abstract

Despite certain structural and biochemical similarities, differences exist in the function of the NF-κB (nuclear factor κB) inhibitory proteins IκBα (inhibitory κBα) and IκBβ. The functional disparity arises in part from variance at the level of gene regulation, and in particular from the substantial induction of IκBα, but not IκBβ, gene expression post-NF-κB activation. In the present study, we probe the differential effects of IL (interleukin)-1β on induction of IκBα and perform the first characterization of the human IκBβ promoter. A consensus NF-κB-binding site, capable of binding NF-κB both in vitro and in vivo, is found in the IκBβ gene 5′ flanking region. However, the IκBβ promoter was not substantially activated by pro-inflammatory cytokines, such as IL-1β and tumour necrosis factor α, that are known to cause strong activation of NF-κB. Furthermore, in contrast with IκBα, NF-κB activation did not increase expression of endogenous IκBβ as assessed by analysis of mRNA and protein levels. Unlike κB-responsive promoters, IκBβ promoter-bound p65 inefficiently recruits RNA polymerase II, which stalls at the promoter. We present evidence that this stalling is likely due to the absence of transcription factor IIH engagement, a prerequisite for RNA polymerase II phosphorylation and transcriptional initiation. Differences in the conformation of promoter-bound NF-κB may underlie the variation in the ability to engage the basal transcriptional apparatus at the IκBβ and κB-responsive promoters. This accounts for the differential expression of IκB family members in response to NF-κB activation and furthers our understanding of the mechanisms involved in transcription factor activity and IκBβ gene regulation.

  • chromatin immunoprecipitation (ChIP)
  • cis-element
  • inhibitory κB (IκB)
  • nuclear factor κB (NF-κB)
  • RNA polymerase II
  • transcription

Abbreviations: ChIP, chromatin immunoprecipitation; CTD, C-terminal domain; DMEM, Dulbecco's modified Eagle's medium; DTT, dithiothreitol; EMSA, electrophoretic mobility-shift assay; FCS, foetal calf serum; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; HEK, human embryonic kidney; IκB, inhibitory κB; IL, interleukin; LTR, long terminal repeat; MCP, monocyte chemoattractant protein; NF-κB, nuclear factor κB; Pol, II, polymerase II; RACE, rapid amplification of cDNA ends; RFP, red fluorescent protein; RHD, Rel homology domain; RLM-5′-RACE, RNA ligase-mediated 5′-RACE; TAD, transcriptional activation domain; TFIIH, transcription factor IIH; TNF, tumour necrosis factor; TSS, transcription start site

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November 2006

Volume: 400 Issue: 1

Biochemical Journal: 400 (1)
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In vivo binding of NF-κB to the IκBβ promoter is insufficient for transcriptional activation
Bryan D. Griffin, Paul N. Moynagh
Biochemical Journal Nov 2006, 400 (1) 115-125; DOI: 10.1042/BJ20060786
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In vivo binding of NF-κB to the IκBβ promoter is insufficient for transcriptional activation
Bryan D. Griffin, Paul N. Moynagh
Biochemical Journal Nov 2006, 400 (1) 115-125; DOI: 10.1042/BJ20060786

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Keywords

chromatin immunoprecipitation (ChIP)
cis-element
inhibitory κB (IκB)
nuclear factor κB (NF-κB)
RNA polymerase II
transcription

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