Variation in Genome-wide NF-kappaB RELA Binding Sites upon Microbial Stimuli and Identification of a Virus Response Profile

Abstract

NF-kB transcription factors are master regulators of the innate immune response. Activated downstream of pathogen recognition receptors, they regulate the expression of genes to help fighting infections as well as recruiting the adaptive immune system. NF-kB responds to a wide variety of signals, but the processes by which stimulus-specificity is attained remain unclear. Here, we characterized the response of one NF-kB member, RELA, to four stimuli mimicking infection in human nasopharyngeal epithelial cells. Comparing genome-wide RELA binding, we observed stimulus-specific sites, although most sites overlapped across stimuli. Specifically, the response to Poly I:C -mimicking viral dsRNA and signalling through TLR3 -induced a distinct RELA profile, binding in the vicinity of antiviral genes and correlating with corresponding gene expression. This group of binding sites was also enriched in not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/247965 doi: bioRxiv preprint first posted online Jan. 16, 2018; 2 Interferon Regulatory Factor (IRF) motifs and showed overlapping with IRFs binding sites. A novel NFkB target, OASL was further validated and showed TLR3-specific activation. This work showed that some RELA DNA binding sites varied in activation response following different stimulations and that interaction with more specialized factors could help achieve this stimulus-specific activity. Our data provide a genomic view of regulated host response to different pathogen stimuli.

Synergistic interactions between NOD receptors and TLRs: Mechanisms and clinical implications

“…A single macrophage is estimated to harbor around 2.5 × 10 5 NF‐κB p65 molecules . On the other hand, ChIP‐seq studies in human cell lines have identified between 10,000 and 70,000 immediately accessible p65 binding sites per haploid set of chromosomes . For instance, Detroit 562 cells analyzed after a 80 min LPS stimulation demonstrate 12,198 p65 binding sites; 14,069 sites are detected in THP‐1 cells after a 60 min TNF stimulation .…”

“…On the other hand, ChIP‐seq studies in human cell lines have identified between 10,000 and 70,000 immediately accessible p65 binding sites per haploid set of chromosomes . For instance, Detroit 562 cells analyzed after a 80 min LPS stimulation demonstrate 12,198 p65 binding sites; 14,069 sites are detected in THP‐1 cells after a 60 min TNF stimulation . Although these estimates are very rough, they indicate that if IκB has been totally degraded, then even a minor part of the available NF‐κB p65 pool is sufficient to saturate accessible NF‐κB p65 binding sites in the genome.…”