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

Nat Immunol. 2011 Nov 20;13(1):95-102. doi: 10.1038/ni.2151.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Binding Sites / genetics
  • Cluster Analysis
  • DNA / chemistry
  • DNA / genetics
  • Databases, Genetic
  • Gene Expression Regulation*
  • Humans
  • Macrophages / metabolism
  • Mice
  • NF-kappa B / genetics
  • NF-kappa B / metabolism*
  • Protein Array Analysis
  • Protein Binding
  • Protein Multimerization


  • NF-kappa B
  • DNA