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Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding.

  • Author(s): Siggers, Trevor
  • Chang, Abraham B
  • Teixeira, Ana
  • Wong, Daniel
  • Williams, Kevin J
  • Ahmed, Bilal
  • Ragoussis, Jiannis
  • Udalova, Irina A
  • Smale, Stephen T
  • Bulyk, Martha L
  • et al.

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The unique DNA-binding properties of distinct NF-κB dimers influence the selective regulation of NF-κB target genes. To more thoroughly investigate these dimer-specific differences, we combined protein-binding microarrays and surface plasmon resonance to evaluate DNA sites recognized by eight different NF-κB dimers. We observed three distinct binding-specificity classes and clarified mechanisms by which dimers might regulate distinct sets of genes. We identified many new nontraditional NF-κB binding site (κB site) sequences and highlight the plasticity of NF-κB dimers in recognizing κB sites with a single consensus half-site. This study provides a database that can be used in efforts to identify NF-κB target sites and uncover gene regulatory circuitry.

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