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


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


Nature Immunology (2011) 13(1), 95-102