In vitro selection of optimal RelB/p52 DNA-binding motifs

Rel/NF-kB dimers of different subunit composition can activate distinct subsets of target genes in vivo, however, the role of DNA recognition in this specificity is not well understood. We set out to study the DNA-binding ability of RelB/p52, the least studied of all NF-kB proteins and the main transcriptionally active product of the alternative NF-kB signaling pathway. We searched for optimal binding sites for RelB/p52 by random site selection method, using full-length proteins expressed in eukaryotic cells. The subset of RelB/p52-binding sequences defines a consensus which is very similar to the classical RelA/p50 consensus. Importantly, each of these binding sites is also recognized by RelA/p50 heterodimer with comparable affinity, questioning the existence of RelB/p52-specific kappa B sites.