The role of lncRNA-BTX in viral replication
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ABSTRACT:
PROVIDER: PRJNA872376 | ENA |
REPOSITORIES: ENA
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Project description:The role of lncRNA-BTX in viral replication
| PRJNA864850 | ENA
Project description:To investigate the function of lncRNA-BTX in the regulation of viral replication , we constructed lncRNA-BTX knockout mice.We separately took the peritoneal macrophages of lncRNA-BTX-/- and lncRNA-BTX+/+ mice, extracted RNA after VSV virus stimulation, and performed RNA-seq.
2022-08-26 | GSE211855 | GEO
Project description:To investigate the function of lncRNA-BTX in the regulation of viral replication , we constructed lncRNA-BTX knockout mice.We separately took the peritoneal macrophages of lncRNA-BTX-/- and lncRNA-BTX+/+ mice, extracted RNA after VSV virus stimulation, and performed RNA-seq.
2022-08-06 | GSE210269 | GEO
Project description:Virus-induced lncRNA-BTX allows viral replication by regulating intracellular translocation of DHX9 and ILF3 to induce innate escape
2023-08-10 | PXD044507 |
Project description:Viruses are known for their extremely compact genomes composed almost entirely of protein-coding genes. Nonetheless, four long noncoding RNAs (lncRNAs) are encoded by human cytomegalovirus (HCMV). Although these RNAs accumulate to high levels during lytic infection, their functions remain largely unknown. Here, we show that HCMV-encoded lncRNA4.9 localizes to the viral nuclear replication compartment, and that its depletion restricts viral DNA replication and viral growth. RNA4.9 is transcribed from the HCMV origin of replication (oriLyt) and forms an RNA-DNA hybrid (R-loop) through its G+C-rich 5’ end, and this may be important for the initiation of viral DNA replication. Furthermore, interference with RNA4.9 expression drastically reduces the levels of the viral single-stranded DNA-binding protein (ssDBP), and overexpression of ssDBP alleviates the inhibition of viral DNA replication and growth caused by RNA4.9 depletion. We also identified a similar, oriLyt-embedded, G+C-rich lncRNA in murine cytomegalovirus (MCMV). Knockdown of this lncRNA interferes with MCMV ssDBP expression and viral DNA replication. These results indicate that HCMV RNA4.9 plays an important role in regulating viral DNA replication by coupling oriLyt activity to ssDBP levels, and that this novel activity may be conserved in other betaherpesviruses.
2020-03-03 | GSE134423 | GEO
Project description:N6–methyladenosine (m6A) is the most abundant internal mRNA modification in eukaryotes, and it plays an important role in RNA metabolism and function. Recent studies have revealed that viral RNA m6A modification can play an anti-viral or pro-viral role in virus life cycle. However, whether m6A methylation can modulate replication of coronaviruses, which contain the largest known RNA genomes, remains elusive. Here, we determined that m6A modifications of porcine epidemic diarrhea coronavirus (PEDV) are exclusively located in the N gene at the 3’-end of genome, and that PEDV infection alters the expression pattern of host proteins involved in m6A modification. Depletion of m6A demethylases significantly increased PEDV replication and gene expression whereas knockdown of m6A methyltransferases slightly decreased PEDV infection. Interestingly, m6A binding proteins YTHDF 2 and 3 significantly inhibited PEDV replication whereas YTHDF1 has an opposite effect. When the major m6A sites in the N gene were mutated, the resultant recombinant PEDVs and PEDV replicons had a significant increase in replication and gene expression. This study illustrates that (i) addition of m6A to PEDV RNA inhibits viral replication, and (ii) both host and viral m6A machinery regulates coronavirus replication.
2022-12-01 | GSE141291 | GEO
Project description:N6–methyladenosine (m6A) is the most abundant internal mRNA modification in eukaryotes, and it plays an important role in RNA metabolism and function. Recent studies have revealed that viral RNA m6A modification can play an anti-viral or pro-viral role depending on the virus. However, whether m6A methylation can modulate replication of coronaviruses, which cause some severe human and animal diseases such as Coronavirus Disease 2019 (COVID-19), remains unknown. Here, we determined that m6A modifications of porcine epidemic diarrhea coronavirus (PEDV) are exclusively located in the N gene at the 3’-end of the genome, and that PEDV infection alters the expression pattern of some host proteins involved in m6A modification. Depletion of m6A demethylases significantly increased PEDV replication and gene expression whereas knockdown of m6A methyltransferases slightly decreased PEDV infection. Interestingly, m6A binding proteins YTHDF 2 and 3 significantly inhibited PEDV replication whereas YTHDF1 has the opposite effect. When the major m6A sites in the N gene were mutated, the resultant recombinant PEDVs and PEDV replicons had a significant increase in replication and gene expression. This study illustrates that (i) addition of m6A to PEDV RNA inhibits viral replication, and (ii) both host and viral m6A machinery regulate coronavirus replication.
2020-05-22 | GSE151020 | GEO
Project description:Recent technical advances have resulted in a significant increase in our understanding of the RNA-binding protein (RBP) repertoire present within eukaryotic cells. A particular focus has been on the RBPs that interact with cellular polyadenylated mRNAs. However, recent studies utilising the same technologies have begun to tease apart the RBP interactome of viral mRNAs, most notably SARS-CoV-2, demonstrating clear similarities but also differences between the RBP profiles of viral and cellular mRNAs. Herein, for the first time we comprehensively mapped the RBPs that associate with the NP mRNA of an influenza A virus. Moreover, we provide evidence that the viral polymerase is essential for the recruitment of RPBs to viral mRNAs through direct polymerase-RBP interactions during transcription. We show that loss of TDP-43, that associates with the viral mRNA, results in a decrease in viral mRNA availability within infected cells, with an impact on the accumulation of viral genomic RNA and the yield of infectious viral particles. Overall, we uncover an important role for TDP-43 in the influenza A virus replication cycle via a direct interaction with viral mRNAs and we demonstrate an essential role of the viral polymerase in orchestrating the assembly of viral mRNPs.
2024-04-16 | PXD049316 | Pride
Project description:Recent technical advances have resulted in a significant increase in our understanding of the RNA-binding protein (RBP) repertoire present within eukaryotic cells. A particular focus has been on the RBPs that interact with cellular polyadenylated mRNAs. However, recent studies utilising the same technologies have begun to tease apart the RBP interactome of viral mRNAs, most notably SARS-CoV-2, demonstrating clear similarities but also differences between the RBP profiles of viral and cellular mRNAs. Herein, for the first time we comprehensively mapped the RBPs that associate with the NP mRNA of an influenza A virus. Moreover, we provide evidence that the viral polymerase is essential for the recruitment of RPBs to viral mRNAs through direct polymerase-RBP interactions during transcription. We show that loss of TDP-43, that associates with the viral mRNA, results in a decrease in viral mRNA availability within infected cells, with an impact on the accumulation of viral genomic RNA and the yield of infectious viral particles. Overall, we uncover an important role for TDP-43 in the influenza A virus replication cycle via a direct interaction with viral mRNAs and we demonstrate an essential role of the viral polymerase in orchestrating the assembly of viral mRNPs.
2024-04-16 | PXD040783 | Pride
Project description:SARS-CoV-2 is a highly transmissible virus that causes COVID-19 disease. Mechanisms of viral pathogenesis include excessive inflammation and viral-induced cell death, resulting in tissue damage. We identified the host E3-ubiquitin ligase TRIM7 as an inhibitor of apoptosis and SARS-CoV-2 replication via ubiquitination of the viral membrane (M) protein. Trim7-/- mice exhibited increased pathology and virus titers associated with epithelial apoptosis and dysregulated immune responses. Mechanistically, TRIM7 ubiquitinates M on K14, which protects cells from cell death. Longitudinal SARS-CoV-2 sequence analysis from infected patients revealed that mutations on M-K14 appeared in circulating variants during the pandemic. The relevance of these mutations was tested in a mouse model. A recombinant M-K14/K15R virus showed reduced viral replication, consistent with the role of K15 in virus assembly, and increased levels of apoptosis associated with the loss of ubiquitination on K14. TRIM7 antiviral activity requires caspase-6 inhibition, linking apoptosis with viral replication and pathology.
2024-07-31 | GSE268640 | GEO