Genome reading by the NF-κB transcription factors

The NF-kappa B family of dimeric transcription factors regulates transcription by selectively binding to DNA response elements present within promoters or enhancers of target genes. The DNA response elements, collectively known as kappa B sites or kappa B DNA, share the consensus 5'-GGGRNNNYCC-3' (where R, Y and N are purine, pyrimidine and any nucleotide base, respectively). In addition, several DNA sequences that deviate significantly from the consensus have been shown to accommodate binding by NF-kappa B dimers. X-ray crystal structures of NF-kappa B in complex with diverse kappa B DNA have helped elucidate the chemical principles that underlie target selection in vitro. However, NF-kappa B dimers encounter additional impediments to selective DNA binding in vivo. Work carried out during the past decades has identified some of the barriers to sequence selective DNA target binding within the context of chromatin and suggests possible mechanisms by which NF-kappa B might overcome these obstacles. In this review, we first highlight structural features of NF-kappa B:DNA complexes and how distinctive features of NF-kappa B proteins and DNA sequences contribute to specific complex formation. We then discuss how native NF-kappa B dimers identify DNA binding targets in the nucleus with support from additional factors and how post-translational modifications enable NF-kappa B to selectively bind kappa B sites in vivo.