Studies on PAF1-mediated transcriptional repression of inflammatory genes

Abstract

Transcription of inflammatory genes is tightly regulated to coordinate temporal and spatial control of the inflammatory response. Chromatin modification is one of highlighted regulatory mechanisms involved in the control of inflammatory gene expression. The PAF complex (PAFc), a multifaceted RNA polymerase II (Pol II)-associated factor, has traditionally been considered a transcriptional activator. The composition and function of PAFc are highly conserved from yeast to humans, and this complex affects many steps of transcription, including transcription-related histone modification. Although PAFc was initially considered a general transcription factor associated with Pol II, recent studies have demonstrated that PAFc exerts signal-specific and locus-specific effects. The roles of PAFc in the cell growth with effects on apoptosis and cell cycle have been extensively studied. PAFc has been recently reported to influence developmental signaling, with effects on Notch and Wnt, and immune processes, with effects on the anti-viral response and immune cell differentiation. Based on the upregulation of PAF1 protein levels by stimulation with the pro-inflammatory cytokine IL-1β, I investigated the role of PAF1 in IL-1β-responsive gene expression in HepG2 hepatocarcinoma cells. In resting cells, a subset of IL-1β-inducible genes was repressed by PAF1, which bound the transcription start site of its target genes with paused Pol II and blocked signal-independent recruitment of the GCN5 histone acetyltransferase. Stimulation of the cells with IL-1β activated the transcriptional activator NF-κB, promoting GCN5 recruitment and facilitating acetylation of target gene chromatin. This process dissociated PAF1 from its target genes and allowed productive transcription elongation. A PAF1 deletion mutant that lacked 70 internal amino acids failed to bind chromatin and displayed a defect in target gene repression. Although PAF1 associates with chromatin in combination with other components, target gene repression is largely PAF1-dependent, as it does not require complete integrity of PAFc. IL-1β-induced migration of HepG2 cells was controlled by counteraction between GCN5 and PAF1, which is consistent with the opposing effects of these proteins on IL-1β-inducible gene expression. Although the role of PAFc in transcriptional activation has been extensively investigated, repressive roles of PAFc have not been well addressed. In this study, I demonstrated that PAF1 represses Pol II paused genes that are inducible by the pro-inflammatory cytokine IL-1β. The data presented here suggest that PAF1-mediated gene repression counteracts the activity of GCN5 to prevent inappropriate gene induction and promote proper activation of the inflammatory response