Limits...
Identification and analysis of differentially-expressed microRNAs in Japanese encephalitis virus-infected PK-15 cells with deep sequencing.

Cai Y, Zhu L, Zhou Y, Liu X, Liu X, Li X, Lang Q, Qiao X, Xu Z - Int J Mol Sci (2015)

Bottom Line: Overall, 132 miRNAs were expressed significantly differently after challenge with JEV: 78 were upregulated and 54 downregulated.The sequencing results for selected miRNAs were confirmed with RT-qPCR.Our findings will underpin further studies of miRNAs' roles in JEV replication and identify potential candidates for antiviral therapies against JEV.

View Article: PubMed Central - PubMed

Affiliation: Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an 625014, China. caiyuhan429197524@126.com.

ABSTRACT
Japanese encephalitis virus (JEV), a mosquito-borne Flavivirus, causes acute viral encephalitis with high morbidity and mortality in humans and animals. MicroRNAs (miRNAs) are small noncoding RNAs that are important modulators of the intricate host-pathogen interaction networks. However, our knowledge of the changes that occur in miRNAs in host cells after JEV infection is still limited. To understand the molecular pathogenesis of JEV at the level of posttranscriptional regulation, we used Illumina deep sequencing to sequence two small RNA libraries prepared from PK-15 cells before and after JEV infection. We identified 522 and 427 miRNAs in the infected and uninfected cells, respectively. Overall, 132 miRNAs were expressed significantly differently after challenge with JEV: 78 were upregulated and 54 downregulated. The sequencing results for selected miRNAs were confirmed with RT-qPCR. GO analysis of the host target genes revealed that these dysregulated miRNAs are involved in complex cellular pathways, including the metabolic pathway, inflammatory response and immune response. To our knowledge, this is the first report of the comparative expression of miRNAs in PK-15 cells after JEV infection. Our findings will underpin further studies of miRNAs' roles in JEV replication and identify potential candidates for antiviral therapies against JEV.

Show MeSH

Related in: MedlinePlus

GO annotation of the predicted miRNA target genes. The figure shows the GO annotation of the upregulated genes (A) and downregulated genes (B) in biological processes, cellular components and molecular functions.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4307358&req=5

ijms-16-02204-f005: GO annotation of the predicted miRNA target genes. The figure shows the GO annotation of the upregulated genes (A) and downregulated genes (B) in biological processes, cellular components and molecular functions.

Mentions: To further our understanding of the physiological functions of the dysregulated miRNAs in response to JEV infection, the potential targets of the up- and down-regulated miRNAs were predicted with two commonly-used miRNA target prediction software programs: TargetScan and miRanda. We found tens of thousands of putative targets in the combined outputs of both programs. All of the predicted target genes of the up- and down-regulated miRNAs were then subjected separately to GO analysis. More upregulated genes (targets of the downregulated miRNAs) than downregulated genes (targets of the upregulated miRNAs) were successfully annotated with the GO analysis. The GO category analysis revealed that the upregulated genes fell into the following categories: inflammatory response, immune response, defense response and stimulus response. The main GO categories for the downregulated genes were cellular process, metabolic process and regulation of biological process (Figure 5). Activation of these biological processes (especially related to inflammatory and immune response) suggests a strong antiviral response of the host, but may also contribute to JEV pathogenesis, resulting in encephalitis.


Identification and analysis of differentially-expressed microRNAs in Japanese encephalitis virus-infected PK-15 cells with deep sequencing.

Cai Y, Zhu L, Zhou Y, Liu X, Liu X, Li X, Lang Q, Qiao X, Xu Z - Int J Mol Sci (2015)

GO annotation of the predicted miRNA target genes. The figure shows the GO annotation of the upregulated genes (A) and downregulated genes (B) in biological processes, cellular components and molecular functions.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4307358&req=5

ijms-16-02204-f005: GO annotation of the predicted miRNA target genes. The figure shows the GO annotation of the upregulated genes (A) and downregulated genes (B) in biological processes, cellular components and molecular functions.
Mentions: To further our understanding of the physiological functions of the dysregulated miRNAs in response to JEV infection, the potential targets of the up- and down-regulated miRNAs were predicted with two commonly-used miRNA target prediction software programs: TargetScan and miRanda. We found tens of thousands of putative targets in the combined outputs of both programs. All of the predicted target genes of the up- and down-regulated miRNAs were then subjected separately to GO analysis. More upregulated genes (targets of the downregulated miRNAs) than downregulated genes (targets of the upregulated miRNAs) were successfully annotated with the GO analysis. The GO category analysis revealed that the upregulated genes fell into the following categories: inflammatory response, immune response, defense response and stimulus response. The main GO categories for the downregulated genes were cellular process, metabolic process and regulation of biological process (Figure 5). Activation of these biological processes (especially related to inflammatory and immune response) suggests a strong antiviral response of the host, but may also contribute to JEV pathogenesis, resulting in encephalitis.

Bottom Line: Overall, 132 miRNAs were expressed significantly differently after challenge with JEV: 78 were upregulated and 54 downregulated.The sequencing results for selected miRNAs were confirmed with RT-qPCR.Our findings will underpin further studies of miRNAs' roles in JEV replication and identify potential candidates for antiviral therapies against JEV.

View Article: PubMed Central - PubMed

Affiliation: Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an 625014, China. caiyuhan429197524@126.com.

ABSTRACT
Japanese encephalitis virus (JEV), a mosquito-borne Flavivirus, causes acute viral encephalitis with high morbidity and mortality in humans and animals. MicroRNAs (miRNAs) are small noncoding RNAs that are important modulators of the intricate host-pathogen interaction networks. However, our knowledge of the changes that occur in miRNAs in host cells after JEV infection is still limited. To understand the molecular pathogenesis of JEV at the level of posttranscriptional regulation, we used Illumina deep sequencing to sequence two small RNA libraries prepared from PK-15 cells before and after JEV infection. We identified 522 and 427 miRNAs in the infected and uninfected cells, respectively. Overall, 132 miRNAs were expressed significantly differently after challenge with JEV: 78 were upregulated and 54 downregulated. The sequencing results for selected miRNAs were confirmed with RT-qPCR. GO analysis of the host target genes revealed that these dysregulated miRNAs are involved in complex cellular pathways, including the metabolic pathway, inflammatory response and immune response. To our knowledge, this is the first report of the comparative expression of miRNAs in PK-15 cells after JEV infection. Our findings will underpin further studies of miRNAs' roles in JEV replication and identify potential candidates for antiviral therapies against JEV.

Show MeSH
Related in: MedlinePlus