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

The unique DNA-binding properties of distinct NF-kappa B dimers influence the selective regulation of NF-kappa B 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-kappa B 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-kappa B binding site (kappa B site) sequences and highlight the plasticity of NF-kappa B dimers in recognizing kappa B sites with a single consensus half-site. This study provides a database that can be used in efforts to identify NF-kappa B target sites and uncover gene regulatory circuitry.