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

Chromosomal locations of miRNAs based on the numbers of total miRNAs (detected in the infected and uninfected cells) and differentially-expressed miRNAs. “ND” means that the genome location of the pre-miRNA has not been determined.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-02204-f003: Chromosomal locations of miRNAs based on the numbers of total miRNAs (detected in the infected and uninfected cells) and differentially-expressed miRNAs. “ND” means that the genome location of the pre-miRNA has not been determined.

Mentions: When a host is infected with a viral pathogen, it produces a strong antiviral response to protect itself. To combat this response, the virus induces a response that facilitates its own replication. The precise changes in the microenvironment inside the host cell caused by viral infection require the exquisite regulation of cellular miRNA expression. In total, 132 miRNAs (including 86 known miRNAs and 46 novel miRNAs) were identified as differentially expressed by ≥2-fold. Of these 132 dysregulated miRNAs, 78 miRNAs (one infection-specific, 77 co-expressed) were upregulated and 54 (six infection-specific, 48 co-expressed) were downregulated in the infected cells relative to the uninfected cells (Figure 2, Table S2 in Supplementary Material). The chromosomal distributions of the 132 unique dysregulated miRNAs corresponding to 148 dysregulated pre-miRNAs are shown in Figure 3. These 148 pre-miRNAs were distributed across nearly all of the pig (Sus scrofa) chromosomes (SSC1–SSC18 and SSCX), excluding SSC8. miRNA expression, determined as the number of dysregulated pre-miRNAs per chromosome, was greatest from SSCX. Of 61 miRNAs located on SSCX that were detected in the infected and uninfected cells, 22 (36.07%) miRNAs have been defined as dysregulated miRNAs. Then, 16 (of 43, 37.21%) dysregulated were located on SSC6.


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)

Chromosomal locations of miRNAs based on the numbers of total miRNAs (detected in the infected and uninfected cells) and differentially-expressed miRNAs. “ND” means that the genome location of the pre-miRNA has not been determined.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-02204-f003: Chromosomal locations of miRNAs based on the numbers of total miRNAs (detected in the infected and uninfected cells) and differentially-expressed miRNAs. “ND” means that the genome location of the pre-miRNA has not been determined.
Mentions: When a host is infected with a viral pathogen, it produces a strong antiviral response to protect itself. To combat this response, the virus induces a response that facilitates its own replication. The precise changes in the microenvironment inside the host cell caused by viral infection require the exquisite regulation of cellular miRNA expression. In total, 132 miRNAs (including 86 known miRNAs and 46 novel miRNAs) were identified as differentially expressed by ≥2-fold. Of these 132 dysregulated miRNAs, 78 miRNAs (one infection-specific, 77 co-expressed) were upregulated and 54 (six infection-specific, 48 co-expressed) were downregulated in the infected cells relative to the uninfected cells (Figure 2, Table S2 in Supplementary Material). The chromosomal distributions of the 132 unique dysregulated miRNAs corresponding to 148 dysregulated pre-miRNAs are shown in Figure 3. These 148 pre-miRNAs were distributed across nearly all of the pig (Sus scrofa) chromosomes (SSC1–SSC18 and SSCX), excluding SSC8. miRNA expression, determined as the number of dysregulated pre-miRNAs per chromosome, was greatest from SSCX. Of 61 miRNAs located on SSCX that were detected in the infected and uninfected cells, 22 (36.07%) miRNAs have been defined as dysregulated miRNAs. Then, 16 (of 43, 37.21%) dysregulated were located on SSC6.

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