Transcriptome analysis of PK-15 cells expressing CSFV NS4A
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA876757 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21420622_1.fastq.gz | Fastqsanger.gz | |||
| SRR21420622_2.fastq.gz | Fastqsanger.gz | |||
| SRR21420623_1.fastq.gz | Fastqsanger.gz | |||
| SRR21420623_2.fastq.gz | Fastqsanger.gz | |||
| SRR21420624_1.fastq.gz | Fastqsanger.gz |
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Project description:We used RNA-seq to investigate the functional role of CSFV NS4A in PK-15 cells.we used RNA-seq to investigate the functional role of CSFV NS4A in PK-15 cells.
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Project description:BackgroundClassical swine fever (CSF) is a severe disease of pigs that results in huge economic losses worldwide and is caused by classical swine fever virus (CSFV). CSFV nonstructural protein 4 A (NS4A) plays a crucial role in infectious CSFV particle formation. However, the function of NS4A during CSFV infection is not well understood. RESULTS: In this study, we used RNA-seq to investigate the functional role of CSFV NS4A in PK-15 cells. A total of 3893 differentially expressed genes (DEGs) were identified in PK-15 cells expressing NS4A compared to cells expressing the empty vector (NC). Twelve DEGs were selected and further verified by RT‒qPCR. GO and KEGG enrichment analyses revealed that these DEGs were associated with multiple biological functions, including cell adhesion, apoptosis, host defence response, the inflammatory response, the immune response, and autophagy. Interestingly, some genes associated with host immune defence and inflammatory response were downregulated, and some genes associated with host apoptosis and autophagy were upregulated.ConclusionCSFV NS4A inhibits the innate immune response, and suppresses the expression of important genes associated with defence response to viruses and inflammatory response, and regulates cell adhesion, apoptosis and autophagy.
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Project description:Porcine circovirus type 2 (PCV2) can cause severe disease in the affected pigs, resulting in massive economic loss for the swine industry. Transcriptomics and proteomics approaches have been widely employed to identify the underlying molecular mechanisms of PCV2 infection. Numerous differentially expressed mRNAs, miRNAs, and proteins, together with their associated signaling pathways, have been identified, paving the way to further validation of their biological functions. Long non-coding RNA (lncRNA) is an important regulator of multiple biological processes. However, rare information regarding its role in the PCV2 infection has been obtained. Hence, in our study, RNA-seq was performed by infecting PK-15 cells with PCV2. Analysis of the differentially expressed genes (DEGs) suggested that cytoskeleton, apoptosis, cell division, and protein phosphorylation were significantly disturbed. Then, using stringent parameters, six lncRNAs were identified. Additionally, the potential targets of the lncRNAs were predicted using both cis- and trans-prediction methods. Interestingly, we found that the HOXB (Homeobox B) gene cluster was probably the target of the lncRNA LOC106505099. Enrichment analysis of the target genes showed that numerous developmental processes were altered during PCV2 infection. Therefore, our study revealed that lncRNAs could affect porcine embryo development through the regulation of the HOXB genes.
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