Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SARS-CoV-2 nsp13 restricts episomal DNA transcription and hepatitis B virus infection

ABSTRACT: Non-structural protein 13 (nsp13), as the helicase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been shown to own multiple functions. Here, we reported that nsp13 could restrict episomal DNA transcription without affecting chromosomal DNA. By using different truncated and mutant forms of nsp13, we demonstrated that its NTPase and helicase activities contributed to episomal DNA transcriptional inhibition. This restriction required direct interaction with episomal DNA. By screening nsp13 interacting proteins, we found that structural maintenance of chromosomes 4 was involved. Given the fact that the episomal DNA of hepatitis B virus (HBV) is the major obstacle for antiviral treatment, we investigated and revealed that nsp13 could significantly restrict HBV replication in vitro and in vivo. In conclusion, our findings demonstrated that SARS-CoV-2 nsp13 can specifically inhibit episomal DNA transcription and can be served as a potential antiviral for HBV infection.

ORGANISM(S): Homo sapiens

PROVIDER: GSE200511 | GEO | 2025/04/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

SARS-CoV-2 nsp13 restricts episomal DNA transcription without affecting chromosomal DNA

Project description:Non-structural protein 13 (nsp13), the helicase of SARS-CoV-2, has been shown to possess multiple functions that are essential for viral replication and is considered an attractive target for the development of novel antiviral drugs. We were initially interested in the interplay between nsp13 and interferon signaling, and found that nsp13 inhibited reporter signal of IFN-β promoter assay. Surprisingly, the ectopic expression of different components of the RIG-I/MDA5 pathway, which were used to stimulate IFN-β promoter, was also mitigated by nsp13. However, endogenous expression of these genes was not affected by nsp13. Interestingly, nsp13 restricted expression of foreign genes originated from plasmid transfection, but failed to inhibit them after chromosome integration. These data together with results from run-off transcription assay and RNA sequencing suggested a specific inhibition of episomal but not chromosomal gene transcription by nsp13. By using different truncated and mutant forms of nsp13, we demonstrated that its NTPase and helicase activities contributed to episomal DNA transcriptional inhibition, And this restriction required direct interaction with episomal DNA. Further, we developed a high-throughput nsp13 drug screening method based on the correlation between the helicase activity and nsp13 inhibition on episomal DNA. This method evaluates the inhibitory effect of compounds on nsp13 by detecting the expression of reporter plasmids after co-transfection with nsp13 plasmids, which is economical and convenient compared with conventional methods. In conclusion, we found that nsp13 can specifically inhibit episomal DNA transcription and developed a high-throughput drug screening method targeting nsp13 to facilitate the development of new antiviral drugs.

2023-06-06 | GSE211851 | GEO

Episomal HBV persistence within transcribed host nuclear chromatin compartments involves HBx

Project description:In hepatocyte nuclei, hepatitis B virus (HBV) genomes occur episomally as covalently closed circular DNA (cccDNA). The HBV X protein (HBx) is required to initiate and maintain HBV replication and acts as host gene trans-regulator. However, functionally relevant spatiotemporal localization and interactions of cccDNA and HBx remain to be understood. This is the first study utilizing circularized chromosome conformation capture (4C) to identify regional virus-host genome interactions. We combined 4C with RNA-seq and ChIP-seq to illuminate the nuclear landscape associated with HBV episomes and HBx. Moreover, we functionally studied HBx-binding to episomal HBV DNA. In human HBV-positive HepaRG hepatocytes, 4C and ChIP revealed specific nuclear localization of HBV episomes and HBx associated with actively transcribed nuclear domains correlating well in size with constrained topological units built up by chromatin fibre loops, which are believed to constitute fundamental cell nuclear architectural units. Interestingly, HBx alone occupied transcribed chromatin domains, and its binding to HBV episomes depended on its C-terminus in vitro. In conclusion, HBx and HBV DNA similarly follow higher-order nuclear assembly patterns, specifically favoring transcriptionally active nuclear compartments. These novel observations may shed light on important unsolved problems: to understand the long-term episomal stability and the facilitation of viral persistence.

2018-04-30 | GSE100400 | GEO

SARS-CoV-2 nsp13 restricts episomal DNA transcription without affecting chromosomal DNA

Project description:SARS-CoV-2 nsp13 restricts episomal DNA transcription without affecting chromosomal DNA

| PRJNA872361 | ENA

Identification of protein interactors of SARS-CoV-2 NSP13 in HEK293T cells

Project description:Non-structural protein 13 (NSP13), as the helicase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been shown to contain NTPase activity, DNA/RNA helicase activity, RNA 5′ triphosphatase activity and innate immunity antagonistic function. To study the function of SARS-CoV-2 NSP13, We detect the NSP13 interaction map in HEK293T cells by IP-MS.

2024-09-21 | PXD033076 | Pride

SARS-CoV-2 nsp13 restricts episomal DNA transcription and hepatitis B virus infection

Project description:SARS-CoV-2 nsp13 restricts episomal DNA transcription and hepatitis B virus infection

| PRJNA824848 | ENA

CRISPR-Cas9 Targeting of Hepatitis B Virus Covalently Closed Circular DNA Generates Transcriptionally Active Episomal Variants

Project description:HBV Episomal Variants after CRISPR-Cas9 Editing

| PRJEB51625 | ENA

RNA-Seq of SARS-CoV-2 Nucleocapsid protein expression in human embryonic kidney cell line HEK293

Project description:The RNA genome of the SARS-CoV-2 virus encodes for four structural proteins, 16 non-structural proteins and nine putative accessory factors. A high throughput analysis of interactions between human and SARS-CoV-2 proteins identified multiple interactions of the structural Nucleocapsid (N) protein with RNA processing factors. The N-protein, which is responsible for packaging of the viral genomic RNA was found to interact with two RNA helicases, UPF1 and MOV10 that are involved in nonsense-mediated mRNA decay (NMD). NMD is a translation-coupled mechanism that targets mRNAs harboring a premature stop codon (PTC) for degradation, thereby serving as a quality control and gene regulatory pathway ensuring transcriptome integrity. Here, we wanted to explore the impact of transiently expressed N protein on the transcriptome of human embryonic kidney cell line HEK293 by RNA-Sequencing. To this end, the SARS-CoV2-N protein was transiently expressed from a pcDNA3.1-HA-N plasmid for 48 hours and the corresponding empty vector was used as a control.

2024-09-16 | E-MTAB-14342 | biostudies-arrayexpress

Experimental and natural evidence of SARS-CoV-2 infection-induced activation of type I interferon responses

Project description:Two highly pathogenic human coronaviruses that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) have evolved proteins that can inhibit host antiviral responses, likely contributing to disease progression and high case-fatality rates. SARS-CoV-2 emerged in December 2019 to cause a global pandemic. Recent studies have shown that SARS-CoV-2 is unable to induce a robust type I interferon (IFN) response in human cells, leading to speculations about the ability of SARS-CoV-2 to inhibit innate antiviral responses. However, innate antiviral responses are dynamic in nature and gene expression levels rapidly change within minutes to hours. In this study, we have performed a time series RNA-seq analysis to identify early virus-host processes. SARS-CoV-2 infection upregulated transcripts for type I IFNs and interferon stimulated genes (ISGs) after 12 hours. Furthermore, we analyzed the ability of SARS-CoV-2 to inhibit type I IFN production and downstream antiviral signaling in human cells. Using exogenous stimuli, we discovered that SARS-CoV-2 is unable to modulate IFNb production and downstream expression of ISGs, such as IRF7 and IFIT1. Thus, data from our study indicate that SARS-CoV-2 may have evolved additional mechanisms, such as masking its nucleic acid from cellular immune response sensors to mount a dampened innate antiviral response. Further studies are required to fully identify the range of immune-modulatory strategies of SARS-CoV-2.

2021-05-20 | GSE151513 | GEO

Pharmacological inhibition of bromodomain and extra-terminal proteins induces NRF-2-mediated inhibition of SARS-CoV-2 replication and is subject to viral antagonism [ATAC-seq]

Project description:Inhibitors of bromodomain and extra-terminal proteins (iBETs), including JQ-1, have been suggested as potential therapeutics against SARS-CoV-2 infection. However, molecular mechanisms underlying JQ-1-induced antiviral activity and its susceptibility to viral antagonism remain incompletely understood. iBET treatment transiently inhibited infection by SARS-CoV-2 variants and SARS-CoV, but not MERS-CoV. Our functional assays confirmed JQ-1-mediated downregulation of angiotensin-converting enzyme 2 (ACE2) expression and multi-omics analysis uncovered induction of an antiviral NRF-2-mediated cytoprotective response as an additional antiviral component of JQ-1 treatment. Serial passaging of SARS-CoV-2 in the presence of JQ-1 resulted in predominance of ORF6-deficient variants. JQ-1 antiviral activity was transient in human bronchial airway epithelial cells (hBAECs) treated prior to infection and absent when administered therapeutically. We propose that JQ-1 exerts pleiotropic effects that collectively induce a transient antiviral state that is ultimately nullified by an established SARS-CoV-2 infection, raising questions about the clinical suitability of iBETs in the context of COVID-19.

2023-09-18 | GSE239587 | GEO

Pharmacological inhibition of bromodomain and extra-terminal proteins induces NRF-2-mediated inhibition of SARS-CoV-2 replication and is subject to viral antagonism [RNA-Seq]

2023-09-18 | GSE239585 | GEO