Selective Regulation of a Defined Subset of Inflammatory and Immunoregulatory Genes by an NF-κB p50-IκBζ Pathway

SUMMARY The five NF-κB family members and three nuclear IκB proteins play important biological roles, but the mechanisms by which distinct NF-κB and IκB proteins contribute to selective gene transcription remain poorly understood, especially at a genome-scale level. Using nascent transcript RNA-seq, we observed considerable overlap between p50-dependent and IκBζ-dependent genes in Toll-like receptor 4 (TLR4)-activated macrophages. Key immunoregulatory genes, including Il6 , Il1b , Nos2 , Lcn2, and Batf, are among the p50-IκBζ co-dependent genes. IκBζ bound genomic sites occupied by NF-κB dimers at earlier time points. However, p50-IκBζ co-dependence does not coincide with preferential binding of either p50 or IκBζ, as both proteins and RelA co-occupy thousands of genomic sites. A common feature of p50-IκBζ co-dependent genes is a nearby p50/RelA/IκBζ co-bound site exhibiting p50-dependent binding of both RelA and IκBζ. This result and others suggest that IκBζ may act in concert with RelA:p50 heterodimers. Notably, the IκBζ-dependent and p50-IκBζ-co-dependent genes comprise a high percentage of genes that exhibit the greatest differential expression between TLR4-stimulated and tumor necrosis factor receptor (TNFR)-stimulated macrophages. Thus, our genome-centric analysis reveals a defined p50-IκBζ pathway that selectively activates a set of key immunoregulatory genes and serves as an important contributor to the differential TNFR and TLR4 responses.