129 : IFN-g and TNF alter epigenetic landscapes to control TLR-induced transcriptional responses in macrophages

Abstract

Macrophage activation phenotypes are determined by the interplay between cytokines such as IFN-g or TNF and acute inflammatory stimuli such as TLR ligands. Synergistic activation of inflammatory cytokine genes by IFN-g and TLR signaling is important for innate immunity and inflammatory disease pathogenesis. Enhancement of TLR signaling, a previously proposed mechanism, is insufficient to explain massive synergistic activation of cytokine production in human macrophages. We found that IFN-g induced sustained occupancy of STAT1, IRF-1 and associated histone acetylation at TSS-proximal and distal regulatory elements at the TNF , IL6 and IL12B gene loci in human macrophages. This priming or opening of chromatin did not activate transcription, but greatly increased and prolonged recruitment of TLR4-induced transcription factors and RNA polymerase II to gene promoters and enhancers. Genome-wide analysis revealed pervasive priming of regulatory elements by IFN-g and linked coordinate priming of promoters and enhancers with synergistic induction of transcription. IFN-g-mediated priming conferred sensitivity of cytokine gene transcription to inhibitors of Jak kinases or BET chromatin regulators. These results provide a synergy mechanism whereby IFN-g creates a primed chromatin environment to augment TLR-induced gene transcription, and suggest therapeutic approaches that selectively target priming mechanisms. In contrast, TNF tolerizes macrophages such that inflammatory cytokine genes are not activated in response to subsequent TLR stimulation. Combined genome-wide analysis using RNAseq and ChIPseq identified transcriptional modules that represent subsets of tolerized genes that are regulated by distinct alterations in chromatin states. Overall the results highlight the importance of chromatin-based mechanisms in regulating transcriptional responses to acute stimuli that activate canonical inflammatory signaling pathways.