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Related Experiment Videos

A TNF-induced gene expression program under oscillatory NF-kappaB control.

Bing Tian1, David E Nowak, Allan R Brasier

  • 1Department of Medicine, The University of Texas Medical Branch, Galveston, Texas 77555-1060, USA. bitian@utmb.edu

BMC Genomics
|September 30, 2005
PubMed
Summary
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Tumor necrosis factor (TNF) triggers inflammation via NF-kappaB, which has two activation modes. Oscillatory NF-kappaB activation is essential for late-response genes in epithelial cells.

Area of Science:

  • Molecular Biology
  • Immunology
  • Cell Biology

Background:

  • Tumor necrosis factor (TNF) initiates tissue inflammation via the NF-kappaB transcription factor.
  • NF-kappaB activation can be monophasic or oscillatory, depending on stimulus duration.
  • The temporal expression patterns and distinct gene controls for these NF-kappaB activation modes were not experimentally defined.

Purpose of the Study:

  • To kinetically analyze NF-kappaB-dependent gene expression in response to TNF.
  • To determine if distinct NF-kappaB translocation modes control different gene programs.
  • To characterize the temporal dynamics of the NF-kappaB network in epithelial cells.

Main Methods:

  • Kinetic analysis of microarray data for 74 NF-kappaB-dependent genes.

Related Experiment Videos

  • Hierarchical clustering to identify distinct gene expression profiles (Early, Middle, Late).
  • Validation using Quantitative Real Time PCR (Q-RT-PCR), chromatin immunoprecipitation (ChIP), and bioinformatic analysis.

    • Main Results:

    • Identified distinct "Early", "Middle", and "Late" NF-kappaB-dependent gene expression groups peaking at 1, 3, and 6 hours post-TNF stimulation.
    • Early genes encode cytokines/negative regulators; Late genes encode receptors/adhesion molecules.
    • Oscillatory NF-kappaB activation mode was specifically required for the expression of Late genes.

    Conclusions:

    • NF-kappaB controls sequential, functionally distinct gene expression programs in epithelial cells.
    • The oscillatory activation mode of NF-kappaB is crucial for regulating late-response genes.
    • This provides insights into TNF-regulated genetic responses and NF-kappaB network dynamics.