Selective regulation of a defined subset of inflammatory and immunoregulatory genes by an NF-κB p50-IκBζ pathway

Abstract

The five NF-{kappa}B family members and three nuclear I{kappa}B proteins play important biological roles, but the mechanisms by which distinct NF-{kappa}B and I{kappa}B 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 I{kappa}B{zeta}-dependent genes in Toll-like receptor 4 (TLR4)-activated macrophages. Key immunoregulatory genes, including Il6, Il1b, Nos2, Lcn2, and Batf, are among the p50-I{kappa}B{zeta} co-dependent genes. I{kappa}B{zeta} bound genomic sites occupied by NF-{kappa}B dimers at earlier time points. However, p50-I{kappa}B{zeta} co-dependence does not coincide with preferential binding of either p50 or I{kappa}B{zeta}, as both proteins and RelA co-occupy thousands of genomic sites. A common feature of p50-I{kappa}B{zeta} co-dependent genes is a nearby p50/RelA/I{kappa}B{zeta} co-bound site exhibiting p50-dependent binding of both RelA and I{kappa}B{zeta}. This result and others suggest that I{kappa}B{zeta} may act in concert with RelA:p50 heterodimers. Notably, the I{kappa}B{zeta}-dependent and p50-I{kappa}B{zeta}-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-I{kappa}B{zeta} pathway that selectively activates a set of key immunoregulatory genes and serves as an important contributor to the differential TNFR and TLR4 responses.