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

Abstract

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.

Requirement for the histone deacetylase Hdac3 for the inflammatory gene expression program in macrophages

“…Consistent with this model, basal Stat1 levels are strongly reduced in the tissues of IFN-α/β receptor 1 (IFNAR1) mutant mice (26). In LPS-stimulated cells, the up-regulation of Stat1 expression requires the autocrine and/or paracrine activity of newly synthesized IFN-β (36). Therefore, we hypothesized that a defect in IFN-β production may underlie the observed reduction in Stat1 levels.…”

A dual cis-regulatory code links IRF8 to constitutive and inducible gene expression in macrophages

“…5B) detected a strong enrichment of an IFNb-stimulated gene (ISG) set in wild-type macro- phages. In particular, of the 251 genes in cluster #6, 132 (52.5%) were ISGs (based on either their inducibility by type I IFNs or the requirement of the type I IFN receptor for their activation in response to LPS) (Raza et al 2010;Cheng et al 2011). Seventy-eight of these 132 ISGs were down-regulated also in untreated cells (Fig.…”

Models of signalling networks – what cell biologists can gain from them and give to them

“…How transcription-factor binding sites contribute to gene expression is complicated, but systematic analyses are beginning to suggest that promoter activity is largely a function of binding-site location and multiplicity (MacIsaac et al, 2010;Segal et al, 2008;Sharon et al, 2012). We thus expect that many new computational models will be developed that link signalling dynamics to transcriptional signatures (Cheng et al, 2011;Huang and Fraenkel, 2009). Likewise, as tools advance for studying single cells at the network level, we anticipate improved models of cell-cell communication, cell heterogeneity and multi-cell properties (Anderson et al, 2006;Feinerman et al, 2008;Jørgensen et al, 2009; Box 3.…”