The Specificity of Innate Immune Responses Is Enforced by Repression of Interferon Response Elements by NF-κB p50

The specific binding of transcription factors to cognate sequence elements is thought to be critical for the generation of specific gene expression programs. Members of the nuclear factor kappa B (NF-kappa B) and interferon (IFN) regulatory factor (IRF) transcription factor families bind to the kappa B site and the IFN response element (IRE), respectively, of target genes, and they are activated in macrophages after exposure to pathogens. However, how these factors produce pathogen-specific inflammatory and immune responses remains poorly understood. Combining top-down and bottom-up systems biology approaches, we have identified the NF-kappa B p50 homodimer as a regulator of IRF responses. Unbiased genome-wide expression and biochemical and structural analyses revealed that the p50 homodimer repressed a subset of IFN-inducible genes through a previously uncharacterized subclass of guanine-rich IRE (G-IRE) sequences. Mathematical modeling predicted that the p50 homodimer might enforce the stimulus specificity of composite promoters. Indeed, the production of the antiviral regulator IFN-beta was rendered stimulus-specific by the binding of the p50 homodimer to the G-IRE-containing IFN beta enhancer to suppress cytotoxic IFN signaling. Specifically, a deficiency in p50 resulted in the inappropriate production of IFN-beta in response to bacterial DNA sensed by Toll-like receptor 9. This role for the NF-kappa B p50 homodimer in enforcing the specificity of the cellular response to pathogens by binding to a subset of IRE sequences alters our understanding of how the NF-kappa B and IRF signaling systems cooperate to regulate antimicrobial immunity.