SARS-CoV-2 nsp13 restricts episomal DNA transcription without affecting chromosomal DNA
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA872361 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21170613_1.fastq.gz | Fastqsanger.gz | |||
| SRR21170613_2.fastq.gz | Fastqsanger.gz | |||
| SRR21170614_1.fastq.gz | Fastqsanger.gz | |||
| SRR21170614_2.fastq.gz | Fastqsanger.gz | |||
| SRR21170615_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
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
Project description: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.
2025-04-07 | GSE200511 | GEO
Project description:SARS-CoV-2 nsp13 restricts episomal DNA transcription and hepatitis B virus infection
| PRJNA824848 | ENA
Project description:Nonstructural 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 antivirals. We were initially interested in the interplay between nsp13 and interferon (IFN) signaling, and found that nsp13 inhibited reporter signal in an 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 the expression of foreign genes originating from plasmid transfection, but failed to inhibit them after chromosome integration. These data, together with results from a runoff 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 the inhibition of episomal DNA transcription, and that this restriction required direct interaction with episomal DNA. Based on these findings, we developed an economical and convenient high-throughput drug screening method targeting nsp13. We evaluated the inhibitory effects of various compounds on nsp13 by the expression of reporter gene plasmid after co-transfection with nsp13. 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. IMPORTANCE To combat COVID-19, we need to understand SARS-CoV-2 and develop effective antiviral drugs. In our study, we serendipitously found that SARS-CoV-2 nsp13 could suppress episomal DNA transcription without affecting chromosomal DNA. Detailed characterization revealed that nsp13 suppresses episomal gene expression through its NTPase and helicase functions following DNA binding. Furthermore, we developed a high-throughput drug screening system targeting SARS-CoV-2 nsp13. Compared to traditional SARS-CoV-2 drug screening methods, our system is more economical and convenient, facilitating the development of more potent and selective nsp13 inhibitors and enabling the discovery of new antiviral therapies.
| S-EPMC10373537 | biostudies-literature
Project description:Human induced pluripotent stem (iPS) cells have previously been derived from somatic cells using viral vectors that integrate transgenes into the genome. Genomic integration, however, can allow persistent leaky expression of the transgenes and can create insertional mutations, thus limiting the utility of these cells for both research and clinical applications. Here, we describe the derivation of human iPS cells free of vector and transgene sequences using non-integrating oriP/EBNA1-based episomal vectors. The resulting iPS cells are similar to human embryonic stem (ES) cells in both proliferative and developmental potential. These results demonstrate that reprogramming of human somatic cells does not require genomic integration or the continued presence of exogenous reprogramming factors, and removes one important obstacle to the clinical applications of these cells. This SuperSeries is composed of the following subset Series:; GSE15175: Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 1.c); GSE15176: Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 4.a) Experiment Overall Design: Total 21 samples were analyzed to confirm the similarity of human iPS cells derived with episomal vectors with human ES cells, and a dissimilarity with fibroblasts. Experiment Overall Design: Refer to individual Series
2009-04-04 | E-GEOD-15148 | biostudies-arrayexpress
Project description:The magnitude and determinants of differences in cis-regulation for regulatory sequences residing in episomes versus chromosomes remain almost completely unknown. To address this question in a systematic manner, we developed and applied a novel lentivirus-based massively parallel reporter assay (lentiMPRA) to directly compare the functional activities of 2,236 candidate liver enhancers in an episomal versus a chromosomally integrated context. We find that the activities of chromosomally integrated sequences are substantially different from the activities of the identical sequences assayed on episomes, and furthermore are correlated with different subsets of ENCODE annotations. The results of chromosomally-based reporter assays are also more reproducible and more strongly predictable by both ENCODE annotations and sequence-based models. With a linear model that combines chromatin annotations and sequence information, we achieve a Pearson's R2 of 0.347 for predicting the results of chromosomally integrated reporter assays. This is substantially better than with either chromatin annotations or sequence information alone and also outperforms predictive models of episomal assays. Our results have broad implications for how cis-regulatory elements are identified, prioritized and functionally validated.
2016-10-01 | GSE83894 | GEO
Project description:We examined genome-wide DNA methylation with 20 human iPSC lines derived from five different cell types,and 7 human ESC lines using Illumina’s Infinium HumanMethylation450K and compared among iPSCs by retrovirus, Sendai virus or episomal vectors.
2017-11-06 | GSE73938 | GEO
Project description:Analysis of the episomal backbone's influence on gene expression. The first hypothesis tested in the present study is that the episomal EBNA vectors, which rely on the EBNA-1 oncoprotein for episomal maintenance, have a greater influence on the cells' expression profiles than S/MAR vectors. The second hypothesis tested was that when bacterial sequences are removed from the episomal vector backbone, the gene disturbance is minimal.
2021-12-05 | GSE142299 | GEO
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
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