Research Article: The NF-κB-dependent and -independent transcriptome and chromatin landscapes of human coronavirus 229E-infected cells

Date Published: March 29, 2017

Publisher: Public Library of Science

Author(s): Michael Poppe, Sascha Wittig, Liane Jurida, Marek Bartkuhn, Jochen Wilhelm, Helmut Müller, Knut Beuerlein, Nadja Karl, Sabin Bhuju, John Ziebuhr, M. Lienhard Schmitz, Michael Kracht, Luis Enjuanes.

http://doi.org/10.1371/journal.ppat.1006286

Abstract

Coronavirus replication takes place in the host cell cytoplasm and triggers inflammatory gene expression by poorly characterized mechanisms. To obtain more insight into the signals and molecular events that coordinate global host responses in the nucleus of coronavirus-infected cells, first, transcriptome dynamics was studied in human coronavirus 229E (HCoV-229E)-infected A549 and HuH7 cells, respectively, revealing a core signature of upregulated genes in these cells. Compared to treatment with the prototypical inflammatory cytokine interleukin(IL)-1, HCoV-229E replication was found to attenuate the inducible activity of the transcription factor (TF) NF-κB and to restrict the nuclear concentration of NF-κB subunits by (i) an unusual mechanism involving partial degradation of IKKβ, NEMO and IκBα and (ii) upregulation of TNFAIP3 (A20), although constitutive IKK activity and basal TNFAIP3 expression levels were shown to be required for efficient virus replication. Second, we characterized actively transcribed genomic regions and enhancers in HCoV-229E-infected cells and systematically correlated the genome-wide gene expression changes with the recruitment of Ser5-phosphorylated RNA polymerase II and prototypical histone modifications (H3K9ac, H3K36ac, H4K5ac, H3K27ac, H3K4me1). The data revealed that, in HCoV-infected (but not IL-1-treated) cells, an extensive set of genes was activated without inducible p65 NF-κB being recruited. Furthermore, both HCoV-229E replication and IL-1 were shown to upregulate a small set of genes encoding immunomodulatory factors that bind p65 at promoters and require IKKβ activity and p65 for expression. Also, HCoV-229E and IL-1 activated a common set of 440 p65-bound enhancers that differed from another 992 HCoV-229E-specific enhancer regions by distinct TF-binding motif combinations. Taken together, the study shows that cytoplasmic RNA viruses fine-tune NF-κB signaling at multiple levels and profoundly reprogram the host cellular chromatin landscape, thereby orchestrating the timely coordinated expression of genes involved in multiple signaling, immunoregulatory and metabolic processes.

Partial Text

CoV infect a wide range of host species and cell types, but only six CoV are known to cause disease in humans [1]. Four human coronaviruses, HCoV‑229E, HCoV‑OC43, HCoV‑NL63 and HCoV‑HKU1, are mainly associated with upper respiratory infections, while severe acute respiratory syndrome (SARS)-CoV and middle east respiratory syndrome (MERS)-CoV may cause serious pathology in the lower respiratory tract, with acute lung injury, respiratory failure and death occurring in a significant number of infected individuals [1]. Lung biopsies obtained from SARS patients or infected primates consistently showed increased expression levels of (i) proinflammatory cytokines, such as interleukin(IL)-1, TNF and IL-6, (ii) chemokines, such as IL-8 (CXCL8), IP-10 (CXCL10) and MCP-1 (CCL2) and (iii) several other NF-κB target genes, suggesting that CoV infection triggers prototypical innate immune reactions involving the upregulation of inflammatory genes [2–4]. Other reports revealed a more diverse and incoherent pattern of host cell gene expression in response to SARS-CoV, MERS-CoV and HCoV-229E, respectively [5–7]. To date, it remains unclear if these differences are a consequence of different CoV strains/isolates and cell types being used in the respective studies or result (at least in part) from additional confounding factors, such as paracrine effects of cytokines or chemokines secreted during infection. Studies that define (i) the gene sets that are expressed specifically in CoV-infected but not bystander cells and (ii) the signaling pathways triggered in response to viral replication in these infected cells are still lacking [8]. Also, it remains to be studied if changes in host cellular mRNA levels in infected cells result from differential transcription rates of specific genes, altered mRNA stability, or both mechanisms.

Emerging or re-emerging RNA viruses cause significant morbidity and mortality in humans and animals [1, 32, 33]. With few exceptions, these RNA viruses complete their viral life cycle in the cytoplasm but need to reprogram and/or adjust specific biosynthetic and other pathways required for viral replication and production of infectious virus progeny according to their specific requirements [34, 35]. Simultaneously, intrinsic host cell defense systems are activated and, in many cases, counteracted by a multitude of strategies that viruses developed during viral evolution [32]. Despite significant scientific progress in the past few years, the complete spectrum of interactions between plus-strand RNA viruses and their hosts is far from being understood, in particular if it comes to understanding complex regulatory networks at a genome-wide level [8, 36]. Here, we provide a high-resolution view of both transcriptome and chromatin changes in cells infected with the alphacoronavirus HCoV-229E, a virus that causes mild upper respiratory tract disease and is efficiently transmitted in the human population, indicating excellent adaption to its human host. The sophisticated fine-tuning of IKK-NF-κB activity and the identification of thousands of coronavirus-specific enhancers reported in this study provides important insight into the enormous complexity by which an RNA virus resets the host cell chromatin response to change expression levels of many hundreds of host cell genes and, at the same time, stimulates future studies into the molecular interplay between corona- and other RNA viruses and their hosts.

 

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http://doi.org/10.1371/journal.ppat.1006286

 

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