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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.

Published Web Location

https://doi.org/10.1038/ni.2151
Abstract

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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