Nuclear factor κB (NF-κB) is a family of transcription factors that is involved in inflammatory responses and that regulates hundreds of genes. In vitro reconstitution of NF-κB–mediated transcription requires not only NF-κB, RNA polymerase II, and general transcription factors but also a complex called Mediator. Van Essen et al. created cells in which the Trap-80 subunit of Mediator that binds the p65 subunit of NF-κB was knocked down and, surprisingly, found that the expression of only a subset of NF-κB target genes was lost when cells were exposed to tumor necrosis factor–α (TNF-α). They explored in detail by chromatin immunoprecipitation experiments two Trap-80–dependent genes (Ip-10 and Il-6) and two Trap-80–independent genes (Mip-2 and Nfkbia) and found that the p65 subunit of NF-κB was efficiently recruited to all of the genes regardless of whether Trap-80 was present. However, RNA polymerase II and TFIIB, a component of the preinitiation complex, were not recruited to Trap-80–dependent genes in the absence of Trap-80. To confirm these results, the authors mutated residues in NF-κB that were required to interact with Trap-80 and found that, when expressed in p65 knockout cells, this mutant promoted the expression of the Trap-80–independent Mip-2 gene but not the Trap-80–dependent Ip-10 gene. Chromatin immunoprecipitation experiments showed that the Mip-1, Ip-10, and Nfkbia promoters all bound what the authors call secondary transcription factors—ATF3, c-Jun, Sp1, and JunD—in a p65-dependent fashion in cells exposed to TNF-α. Expression of a fusion protein consisting of the DNA binding domain of p65 and the transcriptional activation domain of Sp1 in p65-knockout cells restored expression of the Trap-80–independent Mip-1 gene but failed to rescue expression of the Trap-80–dependent Ip-10 gene. The authors suggest that NF-κB has two mechanisms for activating gene expression. At some genes, NF-κB directly stimulates expression through its interaction with Mediator. At other genes, it may also license promoters for interaction with secondary transcription factors, which may allow a more persistent transcriptional response. The authors speculate that the direct mechanism may be functioning for NF-κB when bound close to the transcription start site, whereas the indirect mechanism may be important for NF-κB binding to more distal sites.
D. van Essen, B. Engist, G. Natoli, S. Saccani, Two modes of transcriptional activation at native promoters by NF-κB p65. PLoS Biol. 7, e1000073 (2009). [PubMed]