Nice, T. | Search bioRxiv

bioRxiv2026

Lineage-specific chromatin poising enforced by ETS-IRF composite elements determines the divergent interferon responses of plasmacytoid dendritic cells and epithelial cells

Plasmacytoid dendritic cells (pDCs) produce robust type I interferons (IFN-I) within hours of viral sensing, while epithelial cells at mucosal surfaces mount a delayed response dominated by type III interferons (IFN-III). Both cell types express pattern recognition receptors that activate similar downstream transcription factors, yet they produce distinct subsets of IFNs. The mechanisms underlying these differences have remained unclear. Here, using Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) in primary human pDCs and intestinal epithelial cells, we show that IFN-I and IFN-III gene loci carry opposing, constitutively established chromatin accessibility landscapes that determine cell-type-specific interferon induction. The IFN-I locus is broadly open in pDCs and constitutively closed in epithelial cells, while the IFN-III locus displays the reciprocal pattern. Motif enrichment analysis of accessible regions at the IFN-I locus in pDCs revealed unexpected and significant enrichment of ETS family binding motifs alongside IRF motifs, which determines the cell-type-specific locus accessibility. The ETS factor PU.1 and IRF8 bind IFN-I promoters, at composite ETS-IRF elements positioned at the Positive Regulatory Domain IV (PRDIV) site of IFNB1 promoter and adjacent to the TATA-proximal IRF motif of IFNA promoters. IFNL gene promoters lack ETS recognition sequences. PU.1-IRF8 composite factor binding extends across intergenic regions of the IFN-I locus, where candidate enhancer elements marked by H3K4me1, H3K27ac, and RNA Pol II occupancy were identified. We propose that this network of ETS-IRF composite-element-anchored enhancers maintains the IFN-I locus in a constitutively poised state in pDCs, licensing the rapid and robust IFN-I response that defines pDCs. In epithelial cells, the absence of PU.1 and IRF8 renders the IFN-I locus epigenetically silent, while the IFN-III locus is constitutively open. Despite this, the delayed IFN-III gene expression in epithelial cells is due to intrinsically weaker promoter activity relative to IFN-I. These findings reveal that the divergent IFN induction of pDCs and epithelial cells is determined by the chromatin architecture prior to infection. Overall, these observations show that lineage-specific ETS-IRF regulatory factors and promoter strength determine the cell-type-specific IFN activation.

immunology↗

bioRxiv2018

Caspase-mediated cleavage of Murine Norovirus NS1/2 potentiates apoptosis and is required for persistent infection

Human norovirus (HuNoV) is the leading cause of acute gastroenteritis and is spread by fecal shedding that can often persist for weeks to months after infection. Murine norovirus (MNV) is also shed persistently in the feces and provides a tractable model to study molecular mechanisms of enteric persistence. Previous studies have identified non-structural protein 1 (NS1) from the persistent MNV strain CR6 as critical for persistent infection in intestinal epithelial cells (IECs), but its mechanism of action remains unclear. We now find that the function of NS1 in promoting persistence is regulated by apoptosis. Following induction of apoptosis in infected cells, a minority of NS1 is cleaved from the precursor NS1/2 protein, and this cleavage is prevented by mutation of caspase target motifs. MNV strain CR6 with these mutations (CR6{triangleup}casp) is profoundly compromised in infection of IECs and persistence in the intestine. Conversely, replication in tissues outside of the intestine, or in a cultured macrophage cell line, is unchanged, indicating that the requirement of NS1/2 cleavage is intestine-specific. Intriguingly, we also find that cleavage of CR6 NS1/2 potentiates apoptosis, suggesting that regulation of cell death is a novel function of this viral protein. Together, these data indicate that the ability of NS1 to promote MNV persistence in IECs is regulated by host caspases, and suggest that potentiation of apoptosis plays a role in viral tropism in the intestine.\n\nAuthor SummaryHuman Norovirus infection is highly contagious and the most common cause of acute gastroenteritis. Norovirus can persist and be shed for months after infection, leading to continued outbreaks. There are many unanswered questions as to host and viral components of norovirus pathogenesis that can be addressed within the murine norovirus (MNV) model system. We previously identified a critical role for a viral protein, NS1, for intestinal persistence. Herein we describe how the regulation of NS1 is critical for persistent infection in intestinal epithelial cells, but is not required for acute infection of non-epithelial cells, or infection of tissues outside of the gut. Additionally, we demonstrate that NS1 is both regulated by the host cell death machinery, and also reciprocally regulates that machinery to promote cell death during MNV infection, and found that this is specific to persistent strain of MNV. Altogether these data identify a role for how NS1 in a new pathway involved in establishing a persistent norovirus infection in the intestine.

microbiology↗