One Nucleotide in a κB Site Can Determine Cofactor Specificity for NF-κB Dimers

The transcription factor NF-κB regulates a wide variety of genes involved in multiple processes. Although the apparent consensus sequence of DNA binding sites for NF-κB (κB sites) is very broad, the sites active in any one gene show remarkable evolutionary stability. Using a lentivirus-based methodology for implantation of gene regulatory sequences we show that for genes with two κB sites, both are required for activity. Swapping sites between κB-dependent genes altered NF-κB dimer specificity of the promoters and revealed that two κB sites can function together as a module to regulate gene activation. Further, although the sequence of the κB site is important for determining κB family member specificity, rather than determining the ability of a particular dimer to bind effectively, the sequence affects which coactivators will form productive interactions with the bound NF-κB dimer. This suggests that binding sites may impart a specific configuration to bound transcription factors.