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

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.

Aberrant Super‐Enhancer Landscape in Human Hepatocellular Carcinoma

“…To investigate the implications of SE alteration in hepatocarcinogenesis, we compared the SE landscapes between normal adult liver tissue and two HCC cell lines, HepG2 and Huh7. We generated a catalog of SEs from the normal adult liver and from the HepG2 and Huh7 cells based on the publicly available H3K27Ac ChIP‐seq data . Constituent enhancers that occurred within 12.5 kb were stitched and ranked according to their H3K27Ac signal.…”

“…H3K27Ac ChIP‐seq data of HepG2 cells was generated by the Broad Institute and the Bernstein Laboratory . H3K27Ac ChIP‐seq data of Huh7 cells was obtained from a study published by Poppe et al in 2017 . All ChIP‐seq data sets were aligned to the human genome by Bowtie version 0.12.9.…”

Middle East Respiratory Syndrome Coronavirus-Encoded Accessory Proteins Impair MDA5-and TBK1-Mediated Activation of NF-��B

“…As NF-κB plays a critical role in the induction of innate and adaptive immune responses, a number of viruses have evolved to encode antagonists in their genome to prevent or down-regulate NF-κB activation upon infection [25,[45][46][47][48][49] and the same is true of coronaviruses [26,50,51]. Considering the importance of the roles played by NF-κB in the regulation of the host immune responses, it is still possible that MERS-CoV may encode other NF-κB antagonists than ORF4b [26].…”

Loss of IKK subunits limits NF-κB signaling in reovirus infected cells

“…Pathogens therefore have evolved mechanisms to limit its activity. Infection with human coronavirus causes a loss of both IKKβ and NEMO through an unknown mechanism (30). The MCMV protein M45 targets NEMO for autophagolysosomal degradation (31).…”