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

Binding of NF-κB p50 homodimers to an interferon response element restricts interferon signaling and antiviral responses to only the appropriate stimuli. NF-κB Interferes Signaling pathways triggered by pattern recognition receptors elicit gene expression programs that culminate in antiviral or proinflammatory responses. Critical to these are members of the nuclear factor κB (NF-κB) and interferon regulatory factor (IRF) families of transcription factors, which bind to κB sites and interferon response elements (IREs), respectively, in their target genes. In addition to transcriptional activators, the NF-κB family of proteins contains p50, which forms homodimers that act as competitive repressors at κB sites. Noting the importance of transcriptional repressors in preventing inappropriate gene expression, Cheng et al. investigated roles for p50 in immune responses. They showed that p50 homodimers bound to and regulated a subset of IREs that were guanine-rich (G-IREs). Homodimers of p50 set the threshold for the activation of genes by competing with IRFs for binding to G-IREs, effectively acting as promoter “gates” to restrict gene expression to specific stimuli. Together, these data provide evidence of cross-regulation between the main sets of transcription factors that coordinate innate immune responses. 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 κB (NF-κB) and interferon (IFN) regulatory factor (IRF) transcription factor families bind to the κB 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-κB 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-β was rendered stimulus-specific by the binding of the p50 homodimer to the G-IRE–containing IFNβ enhancer to suppress cytotoxic IFN signaling. Specifically, a deficiency in p50 resulted in the inappropriate production of IFN-β in response to bacterial DNA sensed by Toll-like receptor 9. This role for the NF-κB 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-κB and IRF signaling systems cooperate to regulate antimicrobial immunity.